Treatment of reprogramming factor related diseases by inhibition of natural antisense transcript to a reprogramming factor

ABSTRACT

The present invention relates to antisense oligonucleotides that modulate the expression of and/or function of a Reprogramming factor, in particular, by targeting natural antisense polynucleotides of a Reprogramming factor. The invention also relates to the identification of these antisense oligonucleotides and their use in treating diseases and disorders associated with the expression of Reprogramming factors.

The present application claims the priority of U.S. provisional patentapplication 61/179,056 filed May 18, 2009, No. 61/233,996 filed Aug. 14,2009 and U.S. provisional patent application No. 61/286,852 filed Dec.16, 2009 which are incorporated herein by reference in their entireties.

FIELD OF THE INVENTION

Embodiments of the invention comprise oligonucleotides modulatingexpression and/or function of a Reprogramming factor and associatedmolecules.

BACKGROUND

DNA-RNA and RNA-RNA hybridization are important to many aspects ofnucleic acid function including DNA replication, transcription, andtranslation. Hybridization is also central to a variety of technologiesthat either detect a particular nucleic acid or alter its expression.Antisense nucleotides, for example, disrupt gene expression byhybridizing to target RNA, thereby interfering with RNA splicing,transcription, translation, and replication. Antisense DNA has the addedfeature that DNA-RNA hybrids serve as a substrate for digestion byribonuclease H, an activity that is present in most cell types.Antisense molecules can be delivered into cells, as is the case foroligodeoxynucleotides (ODNs), or they can be expressed from endogenousgenes as RNA molecules. The FDA recently approved an antisense drug,VITRAVENE™ (for treatment of cytomegalovirus retinitis), reflecting thatantisense has therapeutic utility.

SUMMARY

In one embodiment, the invention provides methods for inhibiting theaction of a natural antisense transcript by using antisenseoligonucleotide(s) targeted to any region of the natural antisensetranscript resulting in up-regulation of the corresponding sense gene.It is also contemplated herein that inhibition of the natural antisensetranscript can be achieved by siRNA, ribozymes and small molecules,which are considered to be within the scope of the present invention.

One embodiment provides a method of modulating function and/orexpression of a Reprogramming factor polynucleotide in patient cells ortissues in vivo or in vitro comprising contacting said cells or tissueswith an antisense oligonucleotide 5 to 30 nucleotides in length whereinsaid oligonucleotide has at least 50% sequence identity to a reversecomplement of a polynucleotide comprising 5 to 30 consecutivenucleotides within nucleotides 1 to 993 of SEQ ID SEQ ID NO: 4, 1 to 493of SEQ ID NO: 5, and 1 to 418 of SEQ ID NO: 6 thereby modulatingfunction and/or expression of the Reprogramming factor polynucleotide inpatient cells or tissues in vivo or in vitro.

In another embodiment, an oligonucleotide targets a natural antisensesequence of a Reprogramming factor polynucleotide, for example,nucleotides set forth in SEQ ID NO: 4 to 6, and any variants, alleles,homologs, mutants, derivatives, fragments and complementary sequencesthereto. Examples of antisense oligonucleotides are set forth as SEQ IDNOS: 7 to 17.

Another embodiment provides a method of modulating function and/orexpression of a Reprogramming factor polynucleotide in patient cells ortissues in vivo or in vitro comprising contacting said cells or tissueswith an antisense oligonucleotide 5 to 30 nucleotides in length whereinsaid oligonucleotide has at least 50% sequence identity to a reversecomplement of the an antisense of the Reprogramming factorpolynucleotide; thereby modulating function and/or expression of theReprogramming factor polynucleotide in patient cells or tissues in vivoor in vitro.

Another embodiment provides a method of modulating function and/orexpression of a Reprogramming factor polynucleotide in patient cells ortissues in vivo or in vitro comprising contacting said cells or tissueswith an antisense oligonucleotide 5 to 30 nucleotides in length whereinsaid oligonucleotide has at least 50% sequence identity to an antisenseoligonucleotide to a Reprogramming factor antisense polynucleotide;thereby modulating function and/or expression of the Reprogrammingfactor polynucleotide in patient cells or tissues in vivo or in vitro.

In one embodiment, a composition comprises one or more antisenseoligonucleotides which bind to sense and/or antisense Reprogrammingfactor polynucleotides.

In another embodiment, the oligonucleotides comprise one or moremodified or substituted nucleotides.

In another embodiment, the oligonucleotides comprise one or moremodified bonds.

In yet another embodiment, the modified nucleotides comprise modifiedbases comprising phosphorothioate, methylphosphonate, peptide nucleicacids, 2′-O-methyl, fluoro- or carbon, methylene or other locked nucleicacid (LNA) molecules. Preferably, the modified nucleotides are lockednucleic acid molecules, including α-L-LNA.

In another embodiment, the oligonucleotides are administered to apatient subcutaneously, intramuscularly, intravenously orintraperitoneally.

In another embodiment, the oligonucleotides are administered in apharmaceutical composition. A treatment regimen comprises administeringthe antisense compounds at least once to patient; however, thistreatment can be modified to include multiple doses over a period oftime. The treatment can be combined with one or more other types oftherapies.

In another embodiment, the oligonucleotides are encapsulated in aliposome or attached to a carrier molecule (e.g. cholesterol, TATpeptide).

Other aspects are described infra.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1:

FIG. 1A is a graph of real time PCR results showing the fold change +standard deviation in SOX2 mRNA after treatment of HepG2 cells withphosphorothioate oligonucleotides introduced using Lipofectamine 2000,as compared to control. Real time PCR results show that the levels ofSOX2 mRNA in HepG2 cells are significantly increased 48 h aftertreatment with two of the siRNAs designed to SOX2 antisense AI885646.Bars denoted as CUR-0404 and CUR-0406 correspond to samples treated withSEQ ID NOS: 7 and 8 respectively.

FIG. 1B is a graph of real time PCR results showing the fold change +standard deviation in KLF4 mRNA after treatment of HepG2 cells withphosphorothioate oligonucleotides introduced using Lipofectamine 2000,as compared to control. Real time PCR results show that the levels ofKLF4 mRNA in HepG2 cells are significantly increased 48 h aftertreatment with two of the oligos designed to KLF4 antisense. Barsdenoted as CUR-0933, CUR-0931, CUR-0930 and CUR-0932 correspond tosamples treated with SEQ ID NOS: 9 to 12 respectively.

FIG. 1C is a graph of real time PCR results showing the foldchange+standard deviation in POU5F1 mRNA after treatment of HepG2 cellswith phosphorothioate oligonucleotides introduced using Lipofectamine2000, as compared to control. Bars denoted as CUR-1139 to CUR-1143correspond to samples treated with SEQ ID NOS 13 to 17 respectively.

DETAILED DESCRIPTION

Several aspects of the invention are described below with reference toexample applications for illustration. It should be understood thatnumerous specific details, relationships, and methods are set forth toprovide a full understanding of the invention. One having ordinary skillin the relevant art, however, will readily recognize that the inventioncan be practiced without one or more of the specific details or withother methods. The present invention is not limited by the ordering ofacts or events, as some acts may occur in different orders and/orconcurrently with other acts or events. Furthermore, not all illustratedacts or events are required to implement a methodology in accordancewith the present invention.

All genes, gene names, and gene products disclosed herein are intendedto correspond to homologs from any species for which the compositionsand methods disclosed herein are applicable. Thus, the terms include,but are not limited to genes and gene products from humans and mice. Itis understood that when a gene or gene product from a particular speciesis disclosed, this disclosure is intended to be exemplary only, and isnot to be interpreted as a limitation unless the context in which itappears clearly indicates. Thus, for example, for the genes disclosedherein, which in some embodiments relate to mammalian nucleic acid andamino acid sequences are intended to encompass homologous and/ororthologous genes and gene products from other animals including, butnot limited to other mammals, fish, amphibians, reptiles, and birds. Inpreferred embodiments, the genes or nucleic acid sequences are human.

Definitions

The terminology used herein is for the purpose of describing particularembodiments only and is not intended to be limiting of the invention. Asused herein, the singular forms “a”, “an” and “the” are intended toinclude the plural forms as well, unless the context clearly indicatesotherwise. Furthermore, to the extent that the terms “including”,“includes”, “having”, “has”, “with”, or variants thereof are used ineither the detailed description and/or the claims, such terms areintended to be inclusive in a manner similar to the term “comprising.”

The term “about” or “approximately” means within an acceptable errorrange for the particular value as determined by one of ordinary skill inthe art, which will depend in part on how the value is measured ordetermined, i.e., the limitations of the measurement system. Forexample, “about” can mean within 1 or more than 1 standard deviation,per the practice in the art. Alternatively, “about” can mean a range ofup to 20%, preferably up to 10%, more preferably up to 5%, and morepreferably still up to 1% of a given value. Alternatively, particularlywith respect to biological systems or processes, the term can meanwithin an order of magnitude, preferably within 5-fold, and morepreferably within 2-fold, of a value. Where particular values aredescribed in the application and claims, unless otherwise stated theterm “about” meaning within an acceptable error range for the particularvalue should be assumed.

As used herein, the term “mRNA” means the presently known mRNAtranscript(s) of a targeted gene, and any further transcripts which maybe elucidated.

By “antisense oligonucleotides” or “antisense compound” is meant an RNAor DNA molecule that binds to another RNA or DNA (target RNA, DNA). Forexample, if it is an RNA oligonucleotide it binds to another RNA targetby means of RNA-RNA interactions and alters the activity of the targetRNA (Eguchi et al., (1991) Ann. Rev. Biochem. 60, 631-652). An antisenseoligonucleotide can upregulate or downregulate expression and/orfunction of a particular polynucleotide. The definition is meant toinclude any foreign RNA or DNA molecule which is useful from atherapeutic, diagnostic, or other viewpoint. Such molecules include, forexample, antisense RNA or DNA molecules, interference RNA (RNAi), microRNA, decoy RNA molecules, siRNA, enzymatic RNA, therapeutic editing RNAand agonist and antagonist RNA, antisense oligomeric compounds,antisense oligonucleotides, external guide sequence (EGS)oligonucleotides, alternate splicers, primers, probes, and otheroligomeric compounds that hybridize to at least a portion of the targetnucleic acid. As such, these compounds may be introduced in the form ofsingle-stranded, double-stranded, partially single-stranded, or circularoligomeric compounds.

In the context of this invention, the term “oligonucleotide” refers toan oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleicacid (DNA) or mimetics thereof. The term “oligonucleotide”, alsoincludes linear or circular oligomers of natural and/or modifiedmonomers or linkages, including deoxyribonucleosides, ribonucleosides,substituted and alpha-anomeric forms thereof, peptide nucleic acids(PNA), locked nucleic acids (LNA), phosphorothioate, methylphosphonate,and the like. Oligonucleotides are capable of specifically binding to atarget polynucleotide by way of a regular pattern of monomer-to-monomerinteractions, such as Watson-Crick type of base pairing, Hoögsteen orreverse Hoögsteen types of base pairing, or the like.

The oligonucleotide may be “chimeric”, that is, composed of differentregions. In the context of this invention “chimeric” compounds areoligonucleotides, which contain two or more chemical regions, forexample, DNA region(s), RNA region(s), PNA region(s) etc. Each chemicalregion is made up of at least one monomer unit, i.e., a nucleotide inthe case of an oligonucleotides compound. These oligonucleotidestypically comprise at least one region wherein the oligonucleotide ismodified in order to exhibit one or more desired properties. The desiredproperties of the oligonucleotide include, but are not limited, forexample, to increased resistance to nuclease degradation, increasedcellular uptake, and/or increased binding affinity for the targetnucleic acid. Different regions of the oligonucleotide may thereforehave different properties. The chimeric oligonucleotides of the presentinvention can be formed as mixed structures of two or moreoligonucleotides, modified oligonucleotides, oligonucleosides and/oroligonucleotide analogs as described above.

The oligonucleotide can be composed of regions that can be linked in“register” that is, when the monomers are linked consecutively, as innative DNA, or linked via spacers. The spacers are intended toconstitute a covalent “bridge” between the regions and have in preferredcases a length not exceeding about 100 carbon atoms. The spacers maycarry different functionalities, for example, having positive ornegative charge, carry special nucleic acid binding properties(intercalators, groove binders, toxins, fluorophors etc.), beinglipophilic, inducing special secondary structures like, for example,alanine containing peptides that induce alpha-helices.

As used herein “Reprogramming factors” and “Reprogramming factor” areinclusive of all family members, mutants, alleles, fragments, species,coding and noncoding sequences, sense and antisense polynucleotidestrands, etc.

As used herein, the words SOX2, Sox-2, ANOP3, MCOPS3, MGC2413 andTranscription factor SOX-2 are used interchangeably in the presentapplication.

As used herein, the words KLF4, Kruppel-like factor 4 (gut), Epithelialzinc finger protein EZF, EZF, GKLF, Gut-enriched krueppel-like factor,Krueppel-like factor 4 are used interchangeably in the presentapplication.

As used herein, the words POU5F1, Oct-3, Oct-3/4, Oct-4, Octamer-bindingtranscription factor 3, Octamer-binding transcription factor 4, OTF3,OTF4, TOU domain class 5, transcription factor 1′, POU5F1, POU class 5homeobox 1, DADB-104B20.2 and MGC22487 are considered the same in theliterature and are used interchangeably in the present application.

As used herein, the term “oligonucleotide specific for” or“oligonucleotide which targets” refers to an oligonucleotide having asequence (i) capable of forming a stable complex with a portion of thetargeted gene, or (ii) capable of forming a stable duplex with a portionof a mRNA transcript of the targeted gene. Stability of the complexesand duplexes can be determined by theoretical calculations and/or invitro assays. Exemplary assays for determining stability ofhybridization complexes and duplexes are described in the Examplesbelow.

As used herein, the term “target nucleic acid” encompasses DNA, RNA(comprising premRNA and mRNA) transcribed from such DNA, and also cDNAderived from such RNA, coding, noncoding sequences, sense or antisensepolynucleotides. The specific hybridization of an oligomeric compoundwith its target nucleic acid interferes with the normal function of thenucleic acid. This modulation of function of a target nucleic acid bycompounds, which specifically hybridize to it, is generally referred toas “antisense”. The functions of DNA to be interfered include, forexample, replication and transcription. The functions of RNA to beinterfered, include all vital functions such as, for example,translocation of the RNA to the site of protein translation, translationof protein from the RNA, splicing of the RNA to yield one or more mRNAspecies, and catalytic activity which may be engaged in or facilitatedby the RNA. The overall effect of such interference with target nucleicacid function is modulation of the expression of an encoded product oroligonucleotides.

RNA interference “RNAi” is mediated by double stranded RNA (dsRNA)molecules that have sequence-specific homology to their “target” nucleicacid sequences (Caplen, N. J., et al. (2001) Proc. Natl. Acad. Sci. USA98:9742-9747). In certain embodiments of the present invention, themediators are 5-25 nucleotide “small interfering” RNA duplexes (siRNAs).The siRNAs are derived from the processing of dsRNA by an RNase enzymeknown as Dicer (Bernstein, E., et al. (2001) Nature 409:363-366). siRNAduplex products are recruited into a multi-protein siRNA complex termedRISC

(RNA Induced Silencing Complex). Without wishing to be bound by anyparticular theory, a RISC is then believed to be guided to a targetnucleic acid (suitably mRNA), where the siRNA duplex interacts in asequence-specific way to mediate cleavage in a catalytic fashion(Bernstein, E., et al. (2001) Nature 409:363-366; Boutla, A., et al.(2001) Curr Biol. 11:1776-1780). Small interfering RNAs that can be usedin accordance with the present invention can be synthesized and usedaccording to procedures that are well known in the art and that will befamiliar to the ordinarily skilled artisan. Small interfering RNAs foruse in the methods of the present invention suitably comprise betweenabout 1 to about 50 nucleotides (nt). In examples of non limitingembodiments, siRNAs can comprise about 5 to about 40 nt, about 5 toabout 30 nt, about 10 to about 30 nt, about 15 to about 25 nt, or about20-25 nucleotides.

Selection of appropriate oligonucleotides is facilitated by usingcomputer programs that automatically align nucleic acid sequences andindicate regions of identity or homology. Such programs are used tocompare nucleic acid sequences obtained, for example, by searchingdatabases such as GenBank or by sequencing PCR products. Comparison ofnucleic acid sequences from a range of species allows the selection ofnucleic acid sequences that display an appropriate degree of identitybetween species. In the case of genes that have not been sequenced,Southern blots are performed to allow a determination of the degree ofidentity between genes in target species and other species. Byperforming Southern blots at varying degrees of stringency, as is wellknown in the art, it is possible to obtain an approximate measure ofidentity. These procedures allow the selection of oligonucleotides thatexhibit a high degree of complementarity to target nucleic acidsequences in a subject to be controlled and a lower degree ofcomplementarity to corresponding nucleic acid sequences in otherspecies. One skilled in the art will realize that there is considerablelatitude in selecting appropriate regions of genes for use in thepresent invention.

By “enzymatic RNA” is meant an RNA molecule with enzymatic activity(Cech, (1988) J. American. Med. Assoc. 260, 3030-3035). Enzymaticnucleic acids (ribozymes) act by first binding to a target RNA. Suchbinding occurs through the target binding portion of an enzymaticnucleic acid which is held in close proximity to an enzymatic portion ofthe molecule that acts to cleave the target RNA. Thus, the enzymaticnucleic acid first recognizes and then binds a target RNA through basepairing, and once bound to the correct site, acts enzymatically to cutthe target RNA.

By “decoy RNA” is meant an RNA molecule that mimics the natural bindingdomain for a ligand. The decoy RNA therefore competes with naturalbinding target for the binding of a specific ligand. For example, it hasbeen shown that over-expression of HIV trans-activation response (TAR)RNA can act as a “decoy” and efficiently binds HIV tat protein, therebypreventing it from binding to TAR sequences encoded in the HIV RNA(Sullenger et al. (1990) Cell, 63, 601-608). This is meant to be aspecific example. Those in the art will recognize that this is but oneexample, and other embodiments can be readily generated using techniquesgenerally known in the art.

As used herein, the term “monomers” typically indicates monomers linkedby phosphodiester bonds or analogs thereof to form oligonucleotidesranging in size from a few monomeric units, e.g., from about 3-4, toabout several hundreds of monomeric units. Analogs of phosphodiesterlinkages include: phosphorothioate, phosphorodithioate,methylphosphornates, phosphoroselenoate, phosphoramidate, and the like,as more fully described below.

The term “nucleotide” covers naturally occurring nucleotides as well asnonnaturally occurring nucleotides. It should be clear to the personskilled in the art that various nucleotides which previously have beenconsidered “non-naturally occurring” have subsequently been found innature. Thus, “nucleotides” includes not only the known purine andpyrimidine heterocycles-containing molecules, but also heterocyclicanalogues and tautomers thereof. Illustrative examples of other types ofnucleotides are molecules containing adenine, guanine, thymine,cytosine, uracil, purine, xanthine, diaminopurine,8-oxo-N6-methyladenine, 7-deazaxanthine, 7-deazaguanine,N4,N4-ethanocytosin, N6,N6-ethano-2,6-diaminopurine, 5-methylcytosine,5-(C3-C6)-alkynylcytosine, 5-fluorouracil, 5-bromouracil,pseudoisocytosine, 2-hydroxy-5-methyl-4-triazolopyridin, isocytosine,isoguanin, inosine and the “non-naturally occurring” nucleotidesdescribed in Benner et al., U.S. Pat. No. 5,432,272. The term“nucleotide” is intended to cover every and all of these examples aswell as analogues and tautomers thereof. Especially interestingnucleotides are those containing adenine, guanine, thymine, cytosine,and uracil, which are considered as the naturally occurring nucleotidesin relation to therapeutic and diagnostic application in humans.Nucleotides include the natural 2′-deoxy and 2′-hydroxyl sugars, e.g.,as described in Kornberg and Baker, DNA Replication, 2nd Ed. (Freeman,San Francisco, 1992) as well as their analogs.

“Analogs” in reference to nucleotides includes synthetic nucleotideshaving modified base moieties and/or modified sugar moieties (see e.g.,described generally by Scheit, Nucleotide Analogs, John Wiley, New York,1980; Freier & Altmann, (1997) Nucl. Acid. Res., 25(22), 4429-4443,Toulmé, J.J., (2001) Nature Biotechnology 19:17-18; Manoharan M., (1999)Biochemica et Biophysica Acta 1489:117-139; Freier S. M., (1997) NucleicAcid Research, 25:4429-4443, Uhlman, E., (2000) Drug Discovery &Development, 3: 203-213, Herdewin P., (2000) Antisense & Nucleic AcidDrug Dev., 10:297-310); 2′-O, 3′-C-linked [3.2.0]bicycloarabinonucleosides (see e.g. N. K Christiensen., et al, (1998) J.Am. Chem. Soc., 120: 5458-5463; Prakash T P, Bhat B. (2007) Curr Top MedChem. 7(7):641-9; Cho E J, et al. (2009) Annual Review of AnalyticalChemistry, 2, 241-264). Such analogs include synthetic nucleotidesdesigned to enhance binding properties, e.g., duplex or triplexstability, specificity, or the like.

As used herein, “hybridization” means the pairing of substantiallycomplementary strands of oligomeric compounds. One mechanism of pairinginvolves hydrogen bonding, which may be Watson-Crick, Hoögsteen orreversed Hoögsteen hydrogen bonding, between complementary nucleoside ornucleotide bases (nucleotides) of the strands of oligomeric compounds.For example, adenine and thymine are complementary nucleotides whichpair through the formation of hydrogen bonds. Hybridization can occurunder varying circumstances.

An antisense compound is “specifically hybridizable” when binding of thecompound to the target nucleic acid interferes with the normal functionof the target nucleic acid to cause a modulation of function and/oractivity, and there is a sufficient degree of complementarity to avoidnon-specific binding of the antisense compound to non-target nucleicacid sequences under conditions in which specific binding is desired,i.e., under physiological conditions in the case of in vivo assays ortherapeutic treatment, and under conditions in which assays areperformed in the case of in vitro assays.

As used herein, the phrase “stringent hybridization conditions” or“stringent conditions” refers to conditions under which a compound ofthe invention will hybridize to its target sequence, but to a minimalnumber of other sequences. Stringent conditions are sequence-dependentand will be different in different circumstances and in the context ofthis invention, “stringent conditions” under which oligomeric compoundshybridize to a target sequence are determined by the nature andcomposition of the oligomeric compounds and the assays in which they arebeing investigated. In general, stringent hybridization conditionscomprise low concentrations (<0.15M) of salts with inorganic cationssuch as Na++ or K++ (i.e., low ionic strength), temperature higher than20° C.-25° C. below the Tm of the oligomeric compound:target sequencecomplex, and the presence of denaturants such as formamide,dimethylformamide, dimethyl sulfoxide, or the detergent sodium dodecylsulfate (SDS). For example, the hybridization rate decreases 1.1% foreach 1% formamide. An example of a high stringency hybridizationcondition is 0.1× sodium chloride-sodium citrate buffer (SSC)/0.1% (w/v)SDS at 60° C. for 30 minutes.

“Complementary,” as used herein, refers to the capacity for precisepairing between two nucleotides on one or two oligomeric strands. Forexample, if a nucleobase at a certain position of an antisense compoundis capable of hydrogen bonding with a nucleobase at a certain positionof a target nucleic acid, said target nucleic acid being a DNA, RNA, oroligonucleotide molecule, then the position of hydrogen bonding betweenthe oligonucleotide and the target nucleic acid is considered to be acomplementary position. The oligomeric compound and the further DNA,RNA, or oligonucleotide molecule are complementary to each other when asufficient number of complementary positions in each molecule areoccupied by nucleotides which can hydrogen bond with each other. Thus,“specifically hybridizable” and “complementary” are terms which are usedto indicate a sufficient degree of precise pairing or complementarityover a sufficient number of nucleotides such that stable and specificbinding occurs between the oligomeric compound and a target nucleicacid.

It is understood in the art that the sequence of an oligomeric compoundneed not be 100% complementary to that of its target nucleic acid to bespecifically hybridizable. Moreover, an oligonucleotide may hybridizeover one or more segments such that intervening or adjacent segments arenot involved in the hybridization event (e.g., a loop structure,mismatch or hairpin structure). The oligomeric compounds of the presentinvention comprise at least about 70%, or at least about 75%, or atleast about 80%, or at least about 85%, or at least about 90%, or atleast about 95%, or at least about 99% sequence complementarity to atarget region within the target nucleic acid sequence to which they aretargeted. For example, an antisense compound in which 18 of 20nucleotides of the antisense compound are complementary to a targetregion, and would therefore specifically hybridize, would represent 90percent complementarity. In this example, the remaining noncomplementarynucleotides may be clustered or interspersed with complementarynucleotides and need not be contiguous to each other or to complementarynucleotides. As such, an antisense compound which is 18 nucleotides inlength having 4 (four) noncomplementary nucleotides which are flanked bytwo regions of complete complementarity with the target nucleic acidwould have 77.8% overall complementarity with the target nucleic acidand would thus fall within the scope of the present invention. Percentcomplementarity of an antisense compound with a region of a targetnucleic acid can be determined routinely using BLAST programs (basiclocal alignment search tools) and PowerBLAST programs known in the art(Altschul et al., (1990) J. Mol. Biol., 215, 403-410; Zhang and Madden,(1997) Genome Res., 7, 649-656). Percent homology, sequence identity orcomplementarity, can be determined by, for example, the Gap program(Wisconsin Sequence Analysis Package, Version 8 for Unix, GeneticsComputer Group, University Research Park, Madison Wis.), using defaultsettings, which uses the algorithm of Smith and Waterman (Adv. Appl.Math., (1981) 2, 482-489).

As used herein, the term “Thermal Melting Point (Tm)” refers to thetemperature, under defined ionic strength, pH, and nucleic acidconcentration, at which 50% of the oligonucleotides complementary to thetarget sequence hybridize to the target sequence at equilibrium.Typically, stringent conditions will be those in which the saltconcentration is at least about 0.01 to 1.0 M Na ion concentration (orother salts) at pH 7.0 to 8.3 and the temperature is at least about 30°C. for short oligonucleotides (e.g., 10 to 50 nucleotide). Stringentconditions may also be achieved with the addition of destabilizingagents such as formamide.

As used herein, “modulation” means either an increase (stimulation) or adecrease (inhibition) in the expression of a gene.

The term “variant,” when used in the context of a polynucleotidesequence, may encompass a polynucleotide sequence related to a wild typegene. This definition may also include, for example, “allelic,”“splice,” “species,” or “polymorphic” variants. A splice variant mayhave significant identity to a reference molecule, but will generallyhave a greater or lesser number of polynucleotides due to alternatesplicing of exons during mRNA processing. The corresponding polypeptidemay possess additional functional domains or an absence of domains.Species variants are polynucleotide sequences that vary from one speciesto another. Of particular utility in the invention are variants of wildtype gene products. Variants may result from at least one mutation inthe nucleic acid sequence and may result in altered mRNAs or inpolypeptides whose structure or function may or may not be altered. Anygiven natural or recombinant gene may have none, one, or many allelicforms. Common mutational changes that give rise to variants aregenerally ascribed to natural deletions, additions, or substitutions ofnucleotides. Each of these types of changes may occur alone, or incombination with the others, one or more times in a given sequence.

The resulting polypeptides generally will have significant amino acididentity relative to each other. A polymorphic variant is a variation inthe polynucleotide sequence of a particular gene between individuals ofa given species. Polymorphic variants also may encompass “singlenucleotide polymorphisms” (SNPs,) or single base mutations in which thepolynucleotide sequence varies by one base. The presence of SNPs may beindicative of, for example, a certain population with a propensity for adisease state, that is susceptibility versus resistance.

Derivative polynucleotides include nucleic acids subjected to chemicalmodification, for example, replacement of hydrogen by an alkyl, acyl, oramino group. Derivatives, e.g., derivative oligonucleotides, maycomprise non-naturally-occurring portions, such as altered sugarmoieties or inter-sugar linkages. Exemplary among these arephosphorothioate and other sulfur containing species which are known inthe art. Derivative nucleic acids may also contain labels, includingradionucleotides, enzymes, fluorescent agents, chemiluminescent agents,chromogenic agents, substrates, cofactors, inhibitors, magneticparticles, and the like.

A “derivative” polypeptide or peptide is one that is modified, forexample, by glycosylation, pegylation, phosphorylation, sulfation,reduction/alkylation, acylation, chemical coupling, or mild formalintreatment. A derivative may also be modified to contain a detectablelabel, either directly or indirectly, including, but not limited to, aradioisotope, fluorescent, and enzyme label.

As used herein, the term “animal” or “patient” is meant to include, forexample, humans, sheep, elks, deer, mule deer, minks, mammals, monkeys,horses, cattle, pigs, goats, dogs, cats, rats, mice, birds, chicken,reptiles, fish, insects and arachnids.

“Mammal” covers warm blooded mammals that are typically under medicalcare (e.g., humans and domesticated animals). Examples include feline,canine, equine, bovine, and human, as well as just human.

“Treating” or “treatment” covers the treatment of a disease-state in amammal, and includes: (a) preventing the disease-state from occurring ina mammal, in particular, when such mammal is predisposed to thedisease-state but has not yet been diagnosed as having it; (b)inhibiting the disease-state, e.g., arresting it development; and/or (c)relieving the disease-state, e.g., causing regression of the diseasestate until a desired endpoint is reached. Treating also includes theamelioration of a symptom of a disease (e.g., lessen the pain ordiscomfort), wherein such amelioration may or may not be directlyaffecting the disease (e.g., cause, transmission, expression, etc.).

As used herein, “cancer” refers to all types of cancer or neoplasm ormalignant tumors found in mammals, including, but not limited to:leukemias, lymphomas, melanomas, carcinomas and sarcomas. The cancermanifests itself as a “tumor” or tissue comprising malignant cells ofthe cancer. Examples of tumors include sarcomas and carcinomas such as,but not limited to: fibrosarcoma, myxosarcoma, liposarcoma,chondrosarcoma, osteogenic sarcoma, chordoma, angiosarcoma,endotheliosarcoma, lymphangiosarcoma, lymphangioendotheliosarcoma,synovioma, mesothelioma, Ewing's tumor, leiomyosarcoma,rhabdomyosarcoma, colon carcinoma, pancreatic cancer, breast cancer,ovarian cancer, prostate cancer, squamous cell carcinoma, basal cellcarcinoma, adenocarcinoma, sweat gland carcinoma, sebaceous glandcarcinoma, papillary carcinoma, papillary adenocarcinomas,cystadenocarcinoma, medullary carcinoma, bronchogenic carcinoma, renalcell carcinoma, hepatoma, bile duct carcinoma, choriocarcinoma,seminoma, embryonal carcinoma, Wilms' tumor, cervical cancer, testiculartumor, lung carcinoma, small cell lung carcinoma, bladder carcinoma,epithelial carcinoma, glioma, astrocytoma, medulloblastoma,craniopharyngioma, ependymoma, pinealoma, hemangioblastoma, acousticneuroma, oligodendroglioma, meningioma, melanoma, neuroblastoma, andretinoblastoma. Additional cancers which can be treated by the disclosedcomposition according to the invention include but not limited to, forexample, Hodgkin's Disease, Non-Hodgkin's Lymphoma, multiple myeloma,neuroblastoma, breast cancer, ovarian cancer, lung cancer,rhabdomyosarcoma, primary thrombocytosis, primary macroglobulinemia,small-cell lung tumors, primary brain tumors, stomach cancer, coloncancer, malignant pancreatic insulanoma, malignant carcinoid, urinarybladder cancer, premalignant skin lesions, testicular cancer, lymphomas,thyroid cancer, neuroblastoma, esophageal cancer, genitourinary tractcancer, malignant hypercalcemia, cervical cancer, endometrial cancer,adrenal cortical cancer, and prostate cancer.

“Neurological disease or disorder” refers to any disease or disorder ofthe nervous system and/or visual system. “Neurological disease ordisorder” include disease or disorders that involve the central nervoussystem (brain, brainstem and cerebellum), the peripheral nervous system(including cranial nerves), and the autonomic nervous system (parts ofwhich are located in both central and peripheral nervous system).Examples of neurological disorders include but are not limited to,headache, stupor and coma, dementia, seizure, sleep disorders, trauma,infections, neoplasms, neuroopthalmology, movement disorders,demyelinating diseases, spinal cord disorders, and disorders ofperipheral nerves, muscle and neuromuscular junctions. Addiction andmental illness, include, but are not limited to, bipolar disorder andschizophrenia, are also included in the definition of neurologicaldisorder. The following is a list of several neurological disorders,symptoms, signs and syndromes that can be treated using compositions andmethods according to the present invention: acquired epileptiformaphasia; acute disseminated encephalomyelitis; adrenoleukodystrophy;age-related macular degeneration; agenesis of the corpus callosum;agnosia; Aicardi syndrome; Alexander disease; Alpers' disease;alternating hemiplegia; Vascular dementia; amyotrophic lateralsclerosis; anencephaly; Angelman syndrome; angiomatosis; anoxia;aphasia; apraxia; arachnoid cysts; arachnoiditis; Anronl-Chiarimalformation; arteriovenous malformation; Asperger syndrome; ataxiatelegiectasia; attention deficit hyperactivity disorder; autism;autonomic dysfunction; back pain; Batten disease; Behcet's disease;Bell's palsy; benign essential blepharospasm; benign focal; amyotrophy;benign intracranial hypertension; Binswanger's disease; blepharospasm;Bloch Sulzberger syndrome; brachial plexus injury; brain abscess; braininjury; brain tumors (including glioblastoma multiforme); spinal tumor;Brown-Sequard syndrome; Canavan disease; carpal tunnel syndrome;causalgia; central pain syndrome; central pontine myelinolysis; cephalicdisorder; cerebral aneurysm; cerebral arteriosclerosis; cerebralatrophy; cerebral gigantism; cerebral palsy; Charcot-Marie-Toothdisease; chemotherapy-induced neuropathy and neuropathic pain; Chiarimalformation; chorea; chronic inflammatory demyelinating polyneuropathy;chronic pain; chronic regional pain syndrome; Coffin Lowry syndrome;coma, including persistent vegetative state; congenital facial diplegia;corticobasal degeneration; cranial arteritis; craniosynostosis;Creutzfeldt-Jakob disease; cumulative trauma disorders; Cushing'ssyndrome; cytomegalic inclusion body disease; cytomegalovirus infection;dancing eyes-dancing feet syndrome; DandyWalker syndrome; Dawsondisease; De Morsier's syndrome; Dejerine-Klumke palsy; dementia;dermatomyositis; diabetic neuropathy; diffuse sclerosis; dysautonomia;dysgraphia; dyslexia; dystonias; early infantile epilepticencephalopathy; empty sella syndrome; encephalitis; encephaloceles;encephalotrigeminal angiomatosis; epilepsy; Erb's palsy; essentialtremor; Fabry's disease; Fahr's syndrome; fainting; familial spasticparalysis; febrile seizures; Fisher syndrome; Friedreich's ataxia;fronto-temporal dementia and other “tauopathies”; Gaucher's disease;Gerstmann's syndrome; giant cell arteritis; giant cell inclusiondisease; globoid cell leukodystrophy; Guillain-Barre syndrome;HTLV-1-associated myelopathy; Hallervorden-Spatz disease; head injury;headache; hemifacial spasm; hereditary spastic paraplegia; heredopathiaatactic a polyneuritiformis; herpes zoster oticus; herpes zoster;Hirayama syndrome; HIVassociated dementia and neuropathy (alsoneurological manifestations of AIDS); holoprosencephaly; Huntington'sdisease and other polyglutamine repeat diseases; hydranencephaly;hydrocephalus; hypercortisolism; hypoxia; immune-mediatedencephalomyelitis; inclusion body myositis; incontinentia pigmenti;infantile phytanic acid storage disease; infantile refsum disease;infantile spasms; inflammatory myopathy; intracranial cyst; intracranialhypertension; Joubert syndrome; Keams-Sayre syndrome; Kennedy diseaseKinsboume syndrome; Klippel Feil syndrome; Krabbe disease;Kugelberg-Welander disease; kuru; Lafora disease; Lambert-Eatonmyasthenic syndrome; Landau-Kleffner syndrome; lateral medullary(Wallenberg) syndrome; learning disabilities; Leigh's disease;Lennox-Gustaut syndrome; Lesch-Nyhan syndrome; leukodystrophy; Lewy bodydementia; Lissencephaly; locked-in syndrome; Lou Gehrig's disease (i.e.,motor neuron disease or amyotrophic lateral sclerosis); lumbar discdisease; Lyme disease—neurological sequelae; Machado-Joseph disease;macrencephaly; megalencephaly; Melkersson-Rosenthal syndrome; Menieresdisease; meningitis; Menkes disease; metachromatic leukodystrophy;microcephaly; migraine; Miller Fisher syndrome; mini-strokes;mitochondrial myopathies; Mobius syndrome; monomelic amyotrophy; motorneuron disease; Moyamoya disease; mucopolysaccharidoses; milti-infarctdementia; multifocal motor neuropathy; multiple sclerosis and otherdemyelinating disorders; multiple system atrophy with posturalhypotension; p muscular dystrophy; myasthenia gravis; myelinoclasticdiffuse sclerosis; myoclonic encephalopathy of infants; myoclonus;myopathy; myotonia congenital; narcolepsy; neurofibromatosis;neuroleptic malignant syndrome; neurological manifestations of AIDS;neurological sequelae oflupus; neuromyotonia; neuronal ceroidlipofuscinosis; neuronal migration disorders; Niemann-Pick disease;O'Sullivan-McLeod syndrome; occipital neuralgia; occult spinaldysraphism sequence; Ohtahara syndrome; olivopontocerebellar atrophy;opsoclonus myoclonus; optic neuritis; orthostatic hypotension; overusesyndrome; paresthesia; Neurodegenerative disease or disorder(Parkinson's disease, Huntington's disease, Alzheimer's disease,amyotrophic lateral sclerosis (ALS), dementia, multiple sclerosis andother diseases and disorders associated with neuronal cell death);paramyotonia congenital; paraneoplastic diseases; paroxysmal attacks;Parry Romberg syndrome; Pelizaeus-Merzbacher disease; periodicparalyses; peripheral neuropathy; painful neuropathy and neuropathicpain; persistent vegetative state; pervasive developmental disorders;photic sneeze reflex; phytanic acid storage disease; Pick's disease;pinched nerve; pituitary tumors; polymyositis; porencephaly; post-poliosyndrome; postherpetic neuralgia; postinfectious encephalomyelitis;postural hypotension; Prader-Willi syndrome; primary lateral sclerosis;prion diseases; progressive hemifacial atrophy; progressivemultifocalleukoencephalopathy; progressive sclerosing poliodystrophy;progressive supranuclear palsy; pseudotumor cerebri; Ramsay-Huntsyndrome (types I and 11); Rasmussen's encephalitis; reflex sympatheticdystrophy syndrome; Refsum disease; repetitive motion disorders;repetitive stress injuries; restless legs syndrome;retrovirus-associated myelopathy; Rett syndrome; Reye's syndrome; SaintVitus dance; Sandhoff disease; Schilder's disease; schizencephaly;septo-optic dysplasia; shaken baby syndrome; shingles; Shy-Dragersyndrome; Sjogren's syndrome; sleep apnea; Soto's syndrome; spasticity;spina bifida; spinal cord injury; spinal cord tumors; spinal muscularatrophy; Stiff-Person syndrome; stroke; Sturge-Weber syndrome; subacutesclerosing panencephalitis; subcortical arteriosclerotic encephalopathy;Sydenham chorea; syncope; syringomyelia; tardive dyskinesia; Tay-Sachsdisease; temporal arteritis; tethered spinal cord syndrome; Thomsendisease; thoracic outlet syndrome; Tic Douloureux; Todd's paralysis;Tourette syndrome; transient ischemic attack; transmissible spongiformencephalopathies; transverse myelitis; traumatic brain injury; tremor;trigeminal neuralgia; tropical spastic paraparesis; tuberous sclerosis;vascular dementia (multi-infarct dementia); vasculitis includingtemporal arteritis; Von Hippel-Lindau disease; Wallenberg's syndrome;Werdnig-Hoffman disease; West syndrome; whiplash; Williams syndrome;Wildon's disease; and Zellweger syndrome.

An “Inflammation” refers to systemic inflammatory conditions andconditions associated locally with migration and attraction ofmonocytes, leukocytes and/or neutrophils. Examples of inflammationinclude, but are not limited to, Inflammation resulting from infectionwith pathogenic organisms (including gram-positive bacteria,gram-negative bacteria, viruses, fungi, and parasites such as protozoaand helminths), transplant rejection (including rejection of solidorgans such as kidney, liver, heart, lung or cornea, as well asrejection of bone marrow transplants including graft-versus-host disease(GVHD)), or from localized chronic or acute autoimmune or allergicreactions. Autoimmune diseases include acute glomerulonephritis;rheumatoid or reactive arthritis; chronic glomerulonephritis;inflammatory bowel diseases such as Crohn's disease, ulcerative colitisand necrotizing enterocolitis; granulocyte transfusion associatedsyndromes; inflammatory dermatoses such as contact dermatitis, atopicdermatitis, psoriasis; systemic lupus erythematosus (SLE), autoimmunethyroiditis, multiple sclerosis, and some forms of diabetes, or anyother autoimmune state where attack by the subject's own immune systemresults in pathologic tissue destruction. Allergic reactions includeallergic asthma, chronic bronchitis, acute and delayed hypersensitivity.Systemic inflammatory disease states include inflammation associatedwith trauma, burns, reperfusion following ischemic events (e.g.thrombotic events in heart, brain, intestines or peripheral vasculature,including myocardial infarction and stroke), sepsis, ARDS or multipleorgan dysfunction syndrome. Inflammatory cell recruitment also occurs inatherosclerotic plaques. Inflammation includes, but is not limited to,Non-Hodgkin's lymphoma, Wegener's granulomatosis, Hashimoto'sthyroiditis, hepatocellular carcinoma, thymus atrophy, chronicpancreatitis, rheumatoid arthritis, reactive lymphoid hyperplasia,osteoarthritis, ulcerative colitis, papillary carcinoma, Crohn'sdisease, ulcerative colitis, acute cholecystitis, chronic cholecystitis,cirrhosis, chronic sialadenitis, peritonitis, acute pancreatitis,chronic pancreatitis, chronic Gastritis, adenomyosis, endometriosis,acute cervicitis, chronic cervicitis, lymphoid hyperplasia, multiplesclerosis, hypertrophy secondary to idiopathic thrombocytopenic purpura,primary IgA nephropathy, systemic lupus erythematosus, psoriasis,pulmonary emphysema, chronic pyelonephritis, and chronic cystitis.

A cardiovascular disease or disorder includes those disorders that caneither cause ischemia or are caused by reperfusion of the heart.Examples include, but are not limited to, atherosclerosis, coronaryartery disease, granulomatous myocarditis, chronic myocarditis(non-granulomatous), primary hypertrophic cardiomyopathy, peripheralartery disease (PAD), stroke, angina pectoris, myocardial infarction,cardiovascular tissue damage caused by cardiac arrest, cardiovasculartissue damage caused by cardiac bypass, cardiogenic shock, and relatedconditions that would be known by those of ordinary skill in the art orwhich involve dysfunction of or tissue damage to the heart orvasculature, especially, but not limited to, tissue damage related to aReprogramming factor activation. CVS diseases include, but are notlimited to, atherosclerosis, granulomatous myocarditis, myocardialinfarction, myocardial fibrosis secondary to valvular heart disease,myocardial fibrosis without infarction, primary hypertrophiccardiomyopathy, and chronic myocarditis (non-granulomatous).

A “Metabolic disease or disorder” refers to a wide range of diseases anddisorders of the endocrine system including, for example, insulinresistance, diabetes, obesity, impaired glucose tolerance, high bloodcholesterol, hyperglycemia, hyperinsulinemia, dyslipidemia andhyperlipidemia.

Polynucleotide and Oligonucleotide Compositions and Molecules

Targets

In one embodiment, the targets comprise nucleic acid sequences of aReprogramming factor, including without limitation sense and/orantisense noncoding and/or coding sequences associated with aReprogramming factor.

In one embodiment, the targets comprise nucleic acid sequences of SOX2,including without limitation sense and/or antisense noncoding and/orcoding sequences associated with SOX2 gene.

In one embodiment, the targets comprise nucleic acid sequences of KLF4,including without limitation sense and/or antisense noncoding and/orcoding sequences associated with KLF4 gene.

In one embodiment, the targets comprise nucleic acid sequences ofPOU5F1, including without limitation sense and/or antisense noncodingand/or coding sequences associated with POU5F1 gene.

SRY (sex determining region Y)-box 2, also known as SOX2, is atranscription factor that is essential to maintain self-renewal ofundifferentiated embryonic stem cells. This intronless gene encodes amember of the SRY-related HMG-box (SOX) family of transcription factorinvolved in the regulation of embryonic development and in thedetermination of cell fate. The encoded protein may act as atranscriptional activator after forming a protein complex with otherproteins. Mutations in this gene have been associated with bilateralanophthalmia, a severe form of structural eye malformation. This genelies within an intron of another gene called SOX2 overlapping transcript(SOX20T). The ectopic expression of SOX2 may be also related to abnormaldifferentiation of colorectal cancer cells. Sox2 is one of the keytranscription factor required in induced pluripotent stem cells.

A stem cell is a relatively undifferentiated cell that can be induced toproliferate and that can produce progeny that subsequently differentiateinto one or more mature cell types, while also retaining one or morecells with parental developmental potential. In many biologicalinstances, stem cells are also multipotent because they can produceprogeny of more than one distinct cell type. Self-renewal is the otherclassical part of the stem cell definition, and it is essential as usedin this document. In theory, self-renewal can occur by either of twomajor mechanisms. Stem cells may divide asymmetrically, with onedaughter retaining the stem state and the other daughter expressing somedistinct other specific function and phenotype. Alternatively, some ofthe stem cells in a population can divide symmetrically into two stems,thus maintaining some stem cells in the population as a whole, whileother cells in the population give rise to differentiated progeny only.Formally, it is possible that cells that begin as stem cells mightproceed toward a differentiated phenotype, but then “reverse” andre-express the stem cell phenotype.

Progenitor cells have a cellular phenotype that is more primitive (i.e.,is at an earlier step along a developmental pathway or progression thanis a fully differentiated cell). Often, progenitor cells also havesignificant or very high proliferative potential. Progenitor cells maygive rise to multiple distinct differentiated cell types or to a singledifferentiated cell type, depending on the developmental pathway and onthe environment in which the cells develop and differentiate. Like stemcells, it is possible that cells that begin as progenitor cells mightproceed toward a differentiated phenotype, but then “reverse” andre-express the progenitor cell phenotype.

In a preferred embodiment, one or more antisense oligonucleotides bindto a sense and/or antisense polynucleotide of one or more members of thesox family. Examples of the SOX (SRY-related HMG box) family include,for example, Sox-I, Sox-2, Sox-3, Sox-4, Sox6, Sox7, Sox8, Sox9,Sox1˜Sox11, Sox-13, SoxI4, SoxI5, SoxI8, Sox2O, Sox21, Sox30, Sox32 orthe factor Sox-11-D of Xenopus laevis, or a functional fragmentthereof., and a preferred example includes Sox2.

Knippel-like factor 4 (KLF4) is a zinc-finger-containing transcriptionfactor, the expression of which is enriched in the postmitotic cells ofthe intestinal epithelium. KLF4 is a target gene of the tumor suppressoradenomatous polyposis coli (APe). Knippel-like factor 4 (KLF4) isexpressed in a wide variety of tissues in humans, including theintestine and the skin, and is important in many different physiologicprocesses, including development, differentiation, and maintenance ofnormal tissue homeostasis. KLF4 is a bi-functional transcription factorthat can either activate or repress transcription, depending on thetarget gene, and utilizing different mechanisms. In addition, KLF4 canfunction as an oncogene or a tumor suppressor depending on the type ofcancer involved. In concert with three other transcription factors, KLF4can reprogram differentiated fibroblasts into a state resemblingembryonic stem cells in every possible manner tested so far.

Recently, it was found that overexpression of KLF4, in combination withthree other transcription factors could transform mouse fibroblasts intoa state resembling embryonic stem cells (ES cells).

In preferred embodiments, a method of treating diseases or disordersassociated with low levels of Knippel-like factor 4 (KLF4) compriseadministering to a patient an antisense oligonucleotide which increasesKnippel-like factor 4 (KLF4) expression and/or function.

In accordance with embodiments of the invention, the target nucleic acidmolecule is directed to Knippel-like factor 4 (KLF4) and extends to anyof the isoforms, receptors, families and the like of Knippel-like factor4 (KLF4). Synonyms of KLF4 include: Endothelial KruppelLike Zinc FingerProtein (EZF); Gut-Enriched Kruppel-Like Factor (GKLF).

In preferred embodiments, the invention is contemplates all aspectsassociated with the molecules described herein and encompasses allpeptides, polypeptides, derivatives, variants of the polynucleotide andoligonucleotide sequences of KLF4.

In another preferred embodiment, the invention comprises antibodies andaptamers which may be generated to KLF4 molecules.

Octamer binding transcription factor 4 (hereinafter “POU5F1”) belongs tothe POU (Pit-Oct-Unc) family of transcription factors that bind theoctamer motif, a transcription regulatory element found in the promoterand enhancer regions of many genes (Ryan A K, et al. (1997) Genes Dev;11: 1207-1225; Ruvkun G, et al. (1991) Cell 64: 475-478). TheDNA-binding activity of the POU family members is mediated by theso-called POU domain, a bipartite DNA-binding domain consisting of a75-amino acid POU-specific domain, a linker region, and a 60-amino-acidPOU homeodomain (Herr W, et al,. (1995) Genes Dev 9: 1679-1693; ExPASyProteomics Server. Available at http://au.expasy.org/uniprot/Q01860Accessed Jun. 7, 2006; Scholer HR, et al. (1990) Nature 344:435-9.)

POU5F1 has been shown to be critical in the induction and maintenance ofthe pluripotent stem cell state. Downregulation of POU5F1 expression inembryonic stem cells (ESCs) causes them to differentiate and lose theirpluripotency. POU5F1 induces and sustains pluripotency in cooperationwith other transcription factors including SOX2 and NANOG, and alsoplays a crucial role in the early mammalian development. POU5F1 isexpressed at low levels in some adult stem cell populations. (Boiani M,(2005) et al. Nat Rev Mol Cell Biol. 6:872-84.; Boyer L A, et al. (2005)Cell.; 122:947-56.)

The human POU5F1 gene consists of five exons and is located onchromosome 6 in the region of the major histocompatibility complex. Thegene encodes two isoforms, A (POU5F1_iA, also known as OCT-3A) and B(POU5F1_iB, also known as OCT-3B) (Takeda J, et al. (1992) Nucleic AcidsRes 20: 4613-4620).

In some embodiments, the POU5F1 antisense oligonucleotides promote stemcell proliferation.

Induced pluripotent stem (iPS) cells can be obtained from mousefibroblasts by retrovirus-mediated expression of 4 transcriptionfactors, Oct3/4, Sox2, c-Myc and Klf4 and subsequent selection for Fbx15expression Selection for NANOG expression instead of Fbx15 produces iPScells with increased embryonic stem cell-like gene expression and DNAmethylation patterns Expression of the transcription factors Oct4, Sox2,c-Myc, and Klf4 reprograms a somatic genome of fibroblasts to anembryonic pluripotent state. Yu et al. OCT4, SOX2, NANOG, LIN28 aresufficient to reprogram human somatic cells to pluripotent stem cells.The induced pluripotent human stem cells have normal karyotypes,telomerase activity, cell surface markers and typical gene expression ofthe human ES cells, and can differentiate into derivatives of all 3primary germ layers.

In some embodiments, antisense oligonucleotides are used to prevent ortreat diseases or disorders associated with Reprogramming factor familymembers. Exemplary Reprogramming factor mediated diseases and disorderswhich can be treated with cell/tissues regenerated from stem cellsobtained using the antisense compounds comprise: abnormal Reprogrammingfactor expression and/or function, cancer, a renal disease, acardiovascular disease or disorder, inflammation, a neurological diseaseor disorder, scarring, ophthalmic diseases or disorders (e.g.,microphthalmia, coloboma, myopia, anophthalmia/microphthalmia—esophagealatresia syndrome,etc.), Septooptic dysplasia, an autoimmune disease ordisorder, diabetes, atherosclerosis, an immunodeficiency disease, adisease caused by infectious agent (e.g., including, viral, bacterial,fungal, protozoan etc.), a genetic disease (e.g. Duchenne musculardystrophy), a metabolic disease or disorder (e.g. diabetes, obesity,metabolic syndrome, lysosomal disease etc.), trauma (e.g. spinal cordinjury, burns, etc), ischemia, a vascular disease, a hepatic disease ordisorder, Psoriasis, a disease, a disease or disorder requiringtransplantation of cells, tissues, and organs, disorder or conditionrequiring stem cell therapy and a congenital disease or disorder.

In some embodiments, the present invention provides a method forpreparing an induced pluripotent stem cell by reprogramming of a somaticcell, which comprises the step of contacting the aforementionedreprogramming factor with the somatic cell.

There is also provided a method, which comprises the step of adding theaforementioned reprogramming factor to a culture of the somatic cell;the aforementioned method, which comprises the step of introducing agene encoding the aforementioned reprogramming factor into the somaticcell; the aforementioned method, which comprises the step of introducingsaid gene into the somatic cell by using a recombinant vector containingat least one kind of gene encoding the aforementioned reprogrammingfactor; and the aforementioned method, wherein a somatic cell isolatedfrom a patient is used as the somatic cell.

In another aspect, the present invention provides an induced pluripotentstem cell obtained by the aforementioned method. The present inventionalso provides a somatic cell derived by inducing differentiation of theaforementioned induced pluripotent stem cell.

The present invention further provides a method for stem cell therapy,which comprises the step of transplanting a somatic cell, wherein saidcell is obtained by inducing differentiation of an induced pluripotentstem cell obtained by the aforementioned method using a somatic cellisolated and collected from a patient, into said patient. Several kindsof, preferably approximately 200 kinds of iPS cells prepared fromsomatic cells derived from healthy humans can be stored in an iPS cellbank as a library of iPS cells, and one kind or more kinds of the iPScells in the library can be used for preparation of somatic cells,tissues, or organs that are free of rejection by a patient to besubjected to stem cell therapy.

The present invention further provides a method for evaluating aphysiological function or toxicity of a compound, a medicament, a poisonor the like by using various cells obtained by inducing differentiationof an induced pluripotent stem cell obtained by the aforementionedmethod.

The present invention also provides a method for improving ability ofdifferentiation and/or growth of a cell, which comprises the step ofcontacting the aforementioned reprogramming factor with the cell, andfurther provides a cell obtained by the aforementioned method, and asomatic cell derived by inducing differentiation of a cell obtained bythe aforementioned method.

By using the reprogramming factor provided by the present invention,reprogramming of a differentiated cell nucleus can be conveniently andhighly reproducibly induced without using embryos or ES cells, and aninduced pluripotent stem cell, as an undifferentiated cell havingdifferentiation ability, pluripotency, and growth ability similar tothose of ES cells, can be established. For example, an inducedpluripotent stem cell having high growth ability and differentiationpluripotency can be prepared from a patient's own somatic cell by usingthe reprogramming factor of the present invention. Cells obtainable bydifferentiating said cell (for example, cardiac muscle cells, insulinproducing cells, nerve cells and the like) are extremely useful, becausethey can be utilized for stem cell transplantation therapies for avariety of diseases such as cardiac insufficiency, insulin dependentdiabetes mellitus, Parkinson's disease and spinal cord injury, therebythe ethical problem concerning the use of human embryo and rejectionafter transplantation can be avoided. Further, various cells obtainableby differentiating the induced pluripotent stem cell (for example,cardiac muscle cells, hepatic cells and the like) are highly useful assystems for evaluating efficacy or toxicity of compounds, medicaments,poisons and the like.

In some embodiments, the antisense oligonucleotides of the presentinvention are used in conjunction with other transcription factorsrequired to induce pluripotent stem cells from a given adult tissue.These cells can be further introduced into a lesion and allowed todifferentiate into a required cell type in vitro or in vivo.

In some embodiments, the antisense oligonucleotides are administered toa cell or patient to maintain pluripotence and/or self-renewingcharacteristics and is suitable for any stem cell, progenitor cell, orany cell derived. As an illustrative example, any pluripotent human ESCor a respective cell line may be used in the method. Means of deriving apopulation of such cells are well established in the art (ef e.g.Thomson, J. A. et al. [1998] Science 282, 11451147 or Cowan, C. A. etal. [2004] N. Engl. J. Med. 350,1353-1356). Furthermore, 71 independenthuman ESC lines are for example known to exist, of which 11 cell linesare available for research purposes, such as GE01, GE09, BG01, BG02,TE06 or WA09. Adult stem cells may for instance be isolated from bloodfrom the placenta and umbilical cord left over after birth, or frommyofibers, to which they are associated as so called “satellite cells”

Where the method is intended to be used for a progenitor cell, i.e. acell giving rise to mature somatic cells, any progenitor cell may beused in this method of the invention. Examples of suitable progenitorcells include, but are not limited to, neuronal progenitor cells,endothelial progenitor cells, erythroid progenitor cells, cardiacprogenitor cells, oligodendrocyte progenitor cells, retinal progenitorcells, or hematopoietic progenitor cells.

Progenitor cells, such as endothelial progenitor cells obtainable fromperipheral blood, have for example been found to posses high expressionlevels of Nanog and Oct-4. CNS progenitor cells such as retinalprogenitor cells have been reported to express high levels of Sox2.

As indicated above, the antisense oligonucleotides modulate geneexpression and/or function in a cell. In some embodiments an endogenousSOX gene is functionally active. In some of these embodiments therespective cell is a stem or a progenitor cell. Examples of stem cellsthat may be used in the method of the present invention include, but arenot limited to, embryonic stem cells, trophoblast stem cells andextraembryonic stem cells. In some embodiments of the methods of theinvention an ESC (embryonic stem cell), such as an ESC of human origin,i.e. a human ESC may thus be used. In other embodiments the cell is aprogenitor cell. In yet other embodiments the cell is a cancer cell. Anillustrative example of a cancer cell is teratoma cancer cell, such asfor example F9, NTERA2, C3H, TES-1, 1246 (including 1246-3A), SuSa(including SuSal DXRlO and SKOV-3/DXRlO), AT805 (including ATDC5), HTST,HGRT, PC (e.g. PCC3/A/l ) or GCT27. Two further illustrative example ofa cancer cell are a HeLa cell and an MCF-7 cell. In some embodiments thecell is a hybrid cell of a stem cell and a somatic cell. In some ofthese embodiments a cell of an established eukaryotic cell line isselected, such as for instance HEK, COS, CHO, CRE, MT4, DE (duckembryo), QF (quail fibrosarcoma), NSO, BHK, Sf9, PC12, or High 5. Anillustrative example is a HEK 293T cell.

In one embodiment, KLF4 antisense oligonucleotides reprogram stem cellsand modulate self-renewal. Stem cells are contacted with one or moreKLF4 antisense oligonucleotides. For example, overexpression of KLF4 inES cells inhibited differentiation into erythroid progenitors, andincreased their capacity to generate secondary embryoid bodies. Inconcert with Oct3/4 and Sox2, KLF4 activates expression of Lefty], agene expressed in ES cells, but lost during differentiation process.

In another preferred embodiment, one or more antisense KLF4oligonucleotides are administered to one or more stem cells. The cellscan be stem cells isolated from the bone marrow as a progenitor cell, orcells obtained from any other source, such as for example, ATCC.

“Bone marrow derived progenitor cell” (BMDC) or “bone marrow derivedstem cell” refers to a primitive stem cell with the machinery forself-renewal constitutively active. Included in this definition are stemcells that are totipotent, pluripotent and precursors. A “precursorcell” can be any cell in a cell differentiation pathway that is capableof differentiating into a more mature cell. As such, the term “precursorcell population” refers to a group of cells capable of developing into amore mature cell. A precursor cell population can comprise cells thatare totipotent, cells that are pluripotent and cells that are stem celllineage restricted (i.e. cells capable of developing into less than allhematopoietic lineages, or into, for example, only cells of erythroidlineage). As used herein, the term “totipotent cell” refers to a cellcapable of developing into all lineages of cells. Similarly, the term“totipotent population of cells” refers to a composition of cellscapable of developing into all lineages of cells. Also as used herein,the term “pluripotent cell” refers to a cell capable of developing intoa variety (albeit not all) lineages and are at least able to developinto all hematopoietic lineages (e.g., lymphoid, erythroid, andthrombocytic lineages). Bone marrow derived stem cells contain twowell-characterized types of stem cells. Mesenchymal stem cells (MSC)normally form chondrocytes and osteoblasts. Hematopoietic stem cells(HSC) are of mesodermal origin that normally give rise to cells of theblood and immune system (e.g., erythroid, granulocyte/macrophage,magakaryocite and lymphoid lineages). In addition, hematopoietic stemcells also have been shown to have the potential to differentiate intothe cells of the liver (including hepatocytes, bile duct cells), lung,kidney (e.g., renal tubular epithelial cells and renal parenchyma),gastrointestinal tract, skeletal muscle fibers, astrocytes of the eNS,Purkinje neurons, cardiac muscle (e.g., cardiomyocytes), endothelium andskin.

In another preferred embodiment, the antisense oligonucleotides modulatethe expression and/or function of KLF4 in patients suffering from or atrisk of developing diseases or disorders associated with KLF4. Anynumber of diseases or conditions can be treated by modulation of KLF4,including stem cell renewal and re-programming

In other preferred embodiments, the oligomeric compounds of the presentinvention also include variants in which a different base is present atone or more of the nucleotide positions in the compound. For example, ifthe first nucleotide is an adenosine, variants may be produced whichcontain thymidine, guanosine or cytidine at this position. This may bedone at any of the positions of the antisense compound. These compoundsare then tested using the methods described herein to determine theirability to inhibit expression of a target nucleic acid. Antisenseoligonucleotides which modulate expression, activity or any functions ofKLF4 would also modulate factors in cell pathways that are associatedwith KLF4 activity, function or expressIOn.

Examples of factors which are modulated by KLF4 are shown in the tablebelow:

Factor/condition Factor/condition Activation targets Repression targets1200015N20Rik Bax A33 antigen CD11d B2R Cyclin B1 CYP1A1 Cyclin D1Cytokeratin 4 Cyclin E EBVED-L2 Fgf5 hSMVT Histidine decarboxylase lAPKLF2 iNOS Laminin a1 Keratin 4 Nes Keratin 19 Ornithine decarboxylaseKLF4 p53 Laminin-a 3A PAI-1 Laminin-y 1 SM22a Lefty1 SM a-actin NanogSp1 Oct4 p21Cipl p27Kipl p57Kip2 PKG-Ia Rb Sox2 SPRR1A SPRR2A Tbx3 u-PAR

In one embodiment, the oligonucleotides are specific for polynucleotidesof a Reprogramming factor, which includes, without limitation noncodingregions. The Reprogramming factor targets comprise variants of aReprogramming factor; mutants of a Reprogramming factor, including SNPs;noncoding sequences of a Reprogramming factor; alleles, fragments andthe like. Preferably the oligonucleotide is an antisense RNA molecule.

In accordance with embodiments of the invention, the target nucleic acidmolecule is not limited to a Reprogramming factor polynucleotides alonebut extends to any of the isoforms, receptors, homologs, non-codingregions and the like of a Reprogramming factor.

In another embodiment, an oligonucleotide targets a natural antisensesequence (natural antisense to the coding and non-coding regions) of aReprogramming factor targets, including, without limitation, variants,alleles, homologs, mutants, derivatives, fragments and complementarysequences thereto. Preferably the oligonucleotide is an antisense RNA orDNA molecule.

In another embodiment, the oligomeric compounds of the present inventionalso include variants in which a different base is present at one ormore of the nucleotide positions in the compound. For example, if thefirst nucleotide is an adenine, variants may be produced which containthymidine, guanosine, cytidine or other natural or unnatural nucleotidesat this position. This may be done at any of the positions of theantisense compound.

In some embodiments, homology, sequence identity or complementarity,between the antisense compound and target is from about 50% to about60%. In some embodiments, homology, sequence identity orcomplementarity, is from about 60% to about 70%. In some embodiments,homology, sequence identity or complementarity, is from about 70% toabout 80%. In some embodiments, homology, sequence identity orcomplementarity, is from about 80% to about 90%. In some embodiments,homology, sequence identity or complementarity, is about 90%, about 92%,about 94%, about 95%, about 96%, about 97%, about 98%, about 99% orabout 100%.

An antisense compound is specifically hybridizable when binding of thecompound to the target nucleic acid interferes with the normal functionof the target nucleic acid to cause a loss of activity, and there is asufficient degree of complementarity to avoid non-specific binding ofthe antisense compound to non-target nucleic acid sequences underconditions in which specific binding is desired. Such conditionsinclude, i.e., physiological conditions in the case of in vivo assays ortherapeutic treatment, and conditions in which assays are performed inthe case of in vitro assays.

An antisense compound, whether DNA, RNA, chimeric, substituted etc, isspecifically hybridizable when binding of the compound to the target DNAor RNA molecule interferes with the normal function of the target DNA orRNA to cause a loss of utility, and there is a sufficient degree ofcomplementarily to avoid non-specific binding of the antisense compoundto non-target sequences under conditions in which specific binding isdesired, i.e., under physiological conditions in the case of in vivoassays or therapeutic treatment, and in the case of in vitro assays,under conditions in which the assays are performed.

In another preferred embodiment, targeting of a Reprogramming factorincluding without limitation, antisense sequences which are identifiedand expanded, using for example, PCR, hybridization etc., one or more ofthe sequences set forth as SEQ ID NO: 4 to 6, and the like, modulate theexpression or function of a Reprogramming factor. In one embodiment,expression or function is up-regulated as compared to a control. Inanother preferred embodiment expression or function is down-regulated ascompared to a control.

In another preferred embodiment, oligonucleotides comprise nucleic acidsequences set forth as SEQ ID NOS: 7 to 17 including antisense sequenceswhich are identified and expanded, using for example, PCR, hybridizationetc. These oligonucleotides can comprise one or more modifiednucleotides, shorter or longer fragments, modified bonds and the like.Examples of modified bonds or internucleotide linkages comprisephosphorothioate, phosphorodithioate or the like. In another preferredembodiment, the nucleotides comprise a phosphorus derivative. Thephosphorus derivative (or modified phosphate group) which may beattached to the sugar or sugar analog moiety in the modifiedoligonucleotides of the present invention may be a monophosphate,diphosphate, triphosphate, alkylphosphate, alkanephosphate,phosphorothioate and the like. The preparation of the above-notedphosphate analogs, and their incorporation into nucleotides, modifiednucleotides and oligonucleotides, per se, is also known and need not bedescribed here.

The specificity and sensitivity of antisense is also harnessed by thoseof skill in the art for therapeutic uses. Antisense oligonucleotideshave been employed as therapeutic moieties in the treatment of diseasestates in animals and man. Antisense oligonucleotides have been safelyand effectively administered to humans and numerous clinical trials arepresently underway. It is thus established that oligonucleotides can beuseful therapeutic modalities that can be configured to be useful intreatment regimes for treatment of cells, tissues and animals,especially humans.

In embodiments of the present invention oligomeric antisense compounds,particularly oligonucleotides, bind to target nucleic acid molecules andmodulate the expression and/or function of molecules encoded by a targetgene. The functions of DNA to be interfered comprise, for example,replication and transcription. The functions of RNA to be interferedcomprise all vital functions such as, for example, translocation of theRNA to the site of protein translation, translation of protein from theRNA, splicing of the RNA to yield one or more mRNA species, andcatalytic activity which may be engaged in or facilitated by the RNA.The functions may be up-regulated or inhibited depending on thefunctions desired.

The antisense compounds, include, antisense oligomeric compounds,antisense oligonucleotides, external guide sequence (EGS)oligonucleotides, alternate splicers, primers, probes, and otheroligomeric compounds that hybridize to at least a portion of the targetnucleic acid. As such, these compounds may be introduced in the form ofsingle-stranded, double-stranded, partially single-stranded, or circularoligomeric compounds.

Targeting an antisense compound to a particular nucleic acid molecule,in the context of this invention, can be a multistep process. Theprocess usually begins with the identification of a target nucleic acidwhose function is to be modulated. This target nucleic acid may be, forexample, a cellular gene (or mRNA transcribed from the gene) whoseexpression is associated with a particular disorder or disease state, ora nucleic acid molecule from an infectious agent. In the presentinvention, the target nucleic acid encodes a Reprogramming factor.

The targeting process usually also includes determination of at leastone target region, segment, or site within the target nucleic acid forthe antisense interaction to occur such that the desired effect, e.g.,modulation of expression, will result. Within the context of the presentinvention, the term “region” is defined as a portion of the targetnucleic acid having at least one identifiable structure, function, orcharacteristic. Within regions of target nucleic acids are segments.“Segments” are defined as smaller or sub-portions of regions within atarget nucleic acid. “Sites,” as used in the present invention, aredefined as positions within a target nucleic acid.

In one embodiment, the antisense oligonucleotides bind to the naturalantisense sequences of a Reprogramming factor and modulate theexpression and/or function of a Reprogramming factor (SEQ ID NO: 1 to3). Examples of antisense sequences include SEQ ID NOS: 4 to 17.

In another embodiment, the antisense oligonucleotides bind to one ormore segments of a Reprogramming factor polynucleotide and modulate theexpression and/or function of a Reprogramming factor. The segmentscomprise at least five consecutive nucleotides of a Reprogramming factorsense or antisense polynucleotides.

In another embodiment, the antisense oligonucleotides are specific fornatural antisense sequences of a Reprogramming factor wherein binding ofthe oligonucleotides to the natural antisense sequences of aReprogramming factor modulate expression and/or function of aReprogramming factor.

In another embodiment, oligonucleotide compounds comprise sequences setforth as SEQ ID NOS: 7 to 17, antisense sequences which are identifiedand expanded, using for example, PCR, hybridization etc Theseoligonucleotides can comprise one or more modified nucleotides, shorteror longer fragments, modified bonds and the like. Examples of modifiedbonds or internucleotide linkages comprise phosphorothioate,phosphorodithioate or the like. In another preferred embodiment, thenucleotides comprise a phosphorus derivative. The phosphorus derivative(or modified phosphate group) which may be attached to the sugar orsugar analog moiety in the modified oligonucleotides of the presentinvention may be a monophosphate, diphosphate, triphosphate,alkylphosphate, alkanephosphate, phosphorothioate and the like. Thepreparation of the above-noted phosphate analogs, and theirincorporation into nucleotides, modified nucleotides andoligonucleotides, per se, is also known and need not be described here.

Since, as is known in the art, the translation initiation codon istypically 5′-AUG (in transcribed mRNA molecules; 5′-ATG in thecorresponding DNA molecule), the translation initiation codon is alsoreferred to as the “AUG codon,” the “start codon” or the “AUG startcodon”. A minority of genes has a translation initiation codon havingthe RNA sequence 5′-GUG, 5′-UUG or 5′-CUG; and 5′-AUA, 5′-ACG and 5′-CUGhave been shown to function in vivo. Thus, the terms “translationinitiation codon” and “start codon” can encompass many codon sequences,even though the initiator amino acid in each instance is typicallymethionine (in eukaryotes) or formylmethionine (in prokaryotes).Eukaryotic and prokaryotic genes may have two or more alternative startcodons, any one of which may be preferentially utilized for translationinitiation in a particular cell type or tissue, or under a particularset of conditions. In the context of the invention, “start codon” and“translation initiation codon” refer to the codon or codons that areused in vivo to initiate translation of an mRNA transcribed from a geneencoding a Reprogramming factor, regardless of the sequence(s) of suchcodons. A translation termination codon (or “stop codon”) of a gene mayhave one of three sequences, i.e., 5′-UAA, 5′-UAG and 5′-UGA (thecorresponding DNA sequences are 5′-TAA, 5′-TAG and 5′-TGA,respectively).

The terms “start codon region” and “translation initiation codon region”refer to a portion of such an mRNA or gene that encompasses from about25 to about 50 contiguous nucleotides in either direction (i.e., 5′ or3′) from a translation initiation codon. Similarly, the terms “stopcodon region” and “translation termination codon region” refer to aportion of such an mRNA or gene that encompasses from about 25 to about50 contiguous nucleotides in either direction (i.e., 5′ or 3′) from atranslation termination codon. Consequently, the “start codon region”(or “translation initiation codon region”) and the “stop codon region”(or “translation termination codon region”) are all regions that may betargeted effectively with the antisense compounds of the presentinvention.

The open reading frame (ORF) or “coding region,” which is known in theart to refer to the region between the translation initiation codon andthe translation termination codon, is also a region which may betargeted effectively. Within the context of the present invention, atargeted region is the intragenic region encompassing the translationinitiation or termination codon of the open reading frame (ORF) of agene.

Another target region includes the 5′ untranslated region (5′UTR), knownin the art to refer to the portion of an mRNA in the 5′ direction fromthe translation initiation codon, and thus including nucleotides betweenthe 5′ cap site and the translation initiation codon of an mRNA (orcorresponding nucleotides on the gene). Still another target regionincludes the 3′ untranslated region (3′UTR), known in the art to referto the portion of an mRNA in the 3′ direction from the translationtermination codon, and thus including nucleotides between thetranslation termination codon and 3′ end of an mRNA (or correspondingnucleotides on the gene). The 5′ cap site of an mRNA comprises anN7-methylated guanosine residue joined to the 5′-most residue of themRNA via a 5′-5′ triphosphate linkage. The 5′ cap region of an mRNA isconsidered to include the 5′ cap structure itself as well as the first50 nucleotides adjacent to the cap site. Another target region for thisinvention is the 5′ cap region.

Although some eukaryotic mRNA transcripts are directly translated, manycontain one or more regions, known as “introns,” which are excised froma transcript before it is translated. The remaining (and thereforetranslated) regions are known as “exons” and are spliced together toform a continuous mRNA sequence. In one embodiment, targeting splicesites, i.e., intron-exon junctions or exon-intron junctions, isparticularly useful in situations where aberrant splicing is implicatedin disease, or where an overproduction of a particular splice product isimplicated in disease. An aberrant fusion junction due to rearrangementor deletion is another embodiment of a target site. mRNA transcriptsproduced via the process of splicing of two (or more) mRNAs fromdifferent gene sources are known as “fusion transcripts”. Introns can beeffectively targeted using antisense compounds targeted to, for example,DNA or pre-mRNA.

In another embodiment, the antisense oligonucleotides bind to codingand/or non-coding regions of a target polynucleotide and modulate theexpression and/or function of the target molecule.

In another embodiment, the antisense oligonucleotides bind to naturalantisense polynucleotides and modulate the expression and/or function ofthe target molecule.

In another embodiment, the antisense oligonucleotides bind to sensepolynucleotides and modulate the expression and/or function of thetarget molecule.

Alternative RNA transcripts can be produced from the same genomic regionof DNA. These alternative transcripts are generally known as “variants”.More specifically, “pre-mRNA variants” are transcripts produced from thesame genomic DNA that differ from other transcripts produced from thesame genomic DNA in either their start or stop position and contain bothintronic and exonic sequence.

Upon excision of one or more exon or intron regions, or portions thereofduring splicing, pre-mRNA variants produce smaller “mRNA variants”.Consequently, mRNA variants are processed pre-mRNA variants and eachunique pre-mRNA variant must always produce a unique mRNA variant as aresult of splicing. These mRNA variants are also known as “alternativesplice variants”. If no splicing of the pre-mRNA variant occurs then thepre-mRNA variant is identical to the mRNA variant.

Variants can be produced through the use of alternative signals to startor stop transcription. Pre-mRNAs and mRNAs can possess more than onestart codon or stop codon. Variants that originate from a pre-mRNA ormRNA that use alternative start codons are known as “alternative startvariants” of that pre-mRNA or mRNA. Those transcripts that use analternative stop codon are known as “alternative stop variants” of thatpre-mRNA or mRNA. One specific type of alternative stop variant is the“polyA variant” in which the multiple transcripts produced result fromthe alternative selection of one of the “polyA stop signals” by thetranscription machinery, thereby producing transcripts that terminate atunique polyA sites. Within the context of the invention, the types ofvariants described herein are also embodiments of target nucleic acids.

The locations on the target nucleic acid to which the antisensecompounds hybridize are defined as at least a 5-nucleotide long portionof a target region to which an active antisense compound is targeted.

While the specific sequences of certain exemplary target segments areset forth herein, one of skill in the art will recognize that theseserve to illustrate and describe particular embodiments within the scopeof the present invention. Additional target segments are readilyidentifiable by one having ordinary skill in the art in view of thisdisclosure.

Target segments 5-100 nucleotides in length comprising a stretch of atleast five (5) consecutive nucleotides selected from within theillustrative preferred target segments are considered to be suitable fortargeting as well.

Target segments can include DNA or RNA sequences that comprise at leastthe 5 consecutive nucleotides from the 5′-terminus of one of theillustrative preferred target segments (the remaining nucleotides beinga consecutive stretch of the same DNA or RNA beginning immediatelyupstream of the 5′-terminus of the target segment and continuing untilthe DNA or RNA contains about 5 to about 100 nucleotides). Similarlypreferred target segments are represented by DNA or RNA sequences thatcomprise at least the 5 consecutive nucleotides from the 3′-terminus ofone of the illustrative preferred target segments (the remainingnucleotides being a consecutive stretch of the same DNA or RNA beginningimmediately downstream of the 3′-terminus of the target segment andcontinuing until the DNA or RNA contains about 5 to about 100nucleotides). One having skill in the art armed with the target segmentsillustrated herein will be able, without undue experimentation, toidentify further preferred target segments.

Once one or more target regions, segments or sites have been identified,antisense compounds are chosen which are sufficiently complementary tothe target, i.e., hybridize sufficiently well and with sufficientspecificity, to give the desired effect.

In embodiments of the invention the oligonucleotides bind to anantisense strand of a particular target. The oligonucleotides are atleast 5 nucleotides in length and can be synthesized so eacholigonucleotide targets overlapping sequences such that oligonucleotidesare synthesized to cover the entire length of the target polynucleotide.The targets also include coding as well as non coding regions.

In one embodiment, specific nucleic acids are targeted by antisenseoligonucleotides. Targeting an antisense compound to a particularnucleic acid, is a multistep process. The process usually begins withthe identification of a nucleic acid sequence whose function is to bemodulated. This may be, for example, a cellular gene (or mRNAtranscribed from the gene) whose expression is associated with aparticular disorder or disease state, or a non coding polynucleotidesuch as for example, non coding RNA (ncRNA).

RNAs can be classified into (1) messenger RNAs (mRNAs), which aretranslated into proteins, and (2) non-protein-coding RNAs (ncRNAs).ncRNAs comprise microRNAs, antisense transcripts and otherTranscriptional Units (TU) containing a high density of stop codons andlacking any extensive “Open Reading Frame”. Many ncRNAs appear to startfrom initiation sites in 3′ untranslated regions (3′UTRs) ofprotein-coding loci. ncRNAs are often rare and at least half of thencRNAs that have been sequenced by the FANTOM consortium seem not to bepolyadenylated. Most researchers have for obvious reasons focused onpolyadenylated mRNAs that are processed and exported to the cytoplasm.Recently, it was shown that the set of non-polyadenylated nuclear RNAsmay be very large, and that many such transcripts arise from intergenicregions. The mechanism by which ncRNAs may regulate gene expression isby base pairing with target transcripts. The RNAs that function by basepairing can be grouped into (1) cis encoded RNAs that are encoded at thesame genetic location, but on the opposite strand to the RNAs they actupon and therefore display perfect complementarity to their target, and(2) trans-encoded RNAs that are encoded at a chromosomal locationdistinct from the RNAs they act upon and generally do not exhibitperfect base-pairing potential with their targets.

Without wishing to be bound by theory, perturbation of an antisensepolynucleotide by the antisense oligonucleotides described herein canalter the expression of the corresponding sense messenger RNAs. However,this regulation can either be discordant (antisense knockdown results inmessenger RNA elevation) or concordant (antisense knockdown results inconcomitant messenger RNA reduction). In these cases, antisenseoligonucleotides can be targeted to overlapping or non-overlapping partsof the antisense transcript resulting in its knockdown or sequestration.Coding as well as non-coding antisense can be targeted in an identicalmanner and that either category is capable of regulating thecorresponding sense transcripts —either in a concordant or disconcordantmanner. The strategies that are employed in identifying newoligonucleotides for use against a target can be based on the knockdownof antisense RNA transcripts by antisense oligonucleotides or any othermeans of modulating the desired target

Several nucleotide sequences are relevant to the invention, including:

The following nucleotide sequences are relevant to the invention:

-   -   SEQ ID NO: 1: Homo sapiens SRY (sex determining region Y)-box 2        (SOX2), mRNA (NCBI Accession No.: NM_(—)003106.2).    -   SEQ ID NO: 2: Homo sapiens Kruppel-like factor 4 (gut) (KLF4),        mRNA (NCBI Accession No.: NM_(—)004235.4).    -   SEQ ID NO: 3: Homo sapiens POU class 5 homeobox 1 (POU5F1),        transcript variant 1,mRNA (NCBI Accession No.: NM_(—)002701.4).    -   SEQ ID NO: 4: Human Natural SOX2 antisense sequence (AI885646)    -   SEQ ID NO: 5: Mouse Natural KLF4 antisense sequence (DB461753)    -   SEQ ID NO: 6: Human Natural POU5F1 antisense sequence (AI926793)    -   SOX2 antisense oligonucleotides, SEQ ID NOs: 7 and 8. ‘r’        indicates RNA and * indicates phosphothioate bond.    -   KLF4 antisense oligonucleotides, SEQ ID NOs: 9 to 12. *        indicates phosphothioate bond.    -   POU5F1 antisense oligonucleotides, SEQ ID NOs: 13 to 17. *        indicates phosphothioate bond.    -   FIG. 5 shows the SOX2 sense oligonucleotides, SEQ ID NOs: 18        and 19. The sense oligonucleotides SEQ ID NO: 18 and 19 are the        reverse complements of the antisense oligonucleotides SEQ ID NO:        7 and 8 respectively. ‘r’ indicates RNA.

Strategy 1: In the case of discordant regulation, knocking down theantisense transcript elevates the expression of the conventional (sense)gene. Should that latter gene encode for a known or putative drugtarget, then knockdown of its antisense counterpart could conceivablymimic the action of a receptor agonist or an enzyme stimulant.

Strategy 2: In the case of concordant regulation, one couldconcomitantly knock down both antisense and sense transcripts andthereby achieve synergistic reduction of the conventional (sense) geneexpression. If, for example, an antisense oligonucleotide is used toachieve knockdown, then this strategy can be used to apply one antisenseoligonucleotide targeted to the sense transcript and another antisenseoligonucleotide to the corresponding antisense transcript, or a singleenergetically symmetric antisense oligonucleotide that simultaneouslytargets overlapping sense and antisense transcripts.

According to the present invention, antisense compounds includeantisense oligonucleotides, ribozymes, external guide sequence (EGS)oligonucleotides, siRNA compounds, single- or double-stranded RNAinterference (RNAi) compounds such as siRNA compounds, and otheroligomeric compounds which hybridize to at least a portion of the targetnucleic acid and modulate its function. As such, they may be DNA, RNA,DNA-like, RNA-like, or mixtures thereof, or may be mimetics of one ormore of these. These compounds may be single-stranded, doublestranded,circular or hairpin oligomeric compounds and may contain structuralelements such as internal or terminal bulges, mismatches or loops.Antisense compounds are routinely prepared linearly but can be joined orotherwise prepared to be circular and/or branched. Antisense compoundscan include constructs such as, for example, two strands hybridized toform a wholly or partially double-stranded compound or a single strandwith sufficient self-complementarity to allow for hybridization andformation of a fully or partially double-stranded compound. The twostrands can be linked internally leaving free 3′ or 5′ termini or can belinked to form a continuous hairpin structure or loop. The hairpinstructure may contain an overhang on either the 5′ or 3′ terminusproducing an extension of single stranded character. The double strandedcompounds optionally can include overhangs on the ends. Furthermodifications can include conjugate groups attached to one of thetermini, selected nucleotide positions, sugar positions or to one of theinternucleoside linkages. Alternatively, the two strands can be linkedvia a non-nucleic acid moiety or linker group. When formed from only onestrand, dsRNA can take the form of a self-complementary hairpin-typemolecule that doubles back on itself to form a duplex. Thus, the dsRNAscan be fully or partially double stranded. Specific modulation of geneexpression can be achieved by stable expression of dsRNA hairpins intransgenic cell lines, however, in some embodiments, the gene expressionor function is up regulated. When formed from two strands, or a singlestrand that takes the form of a self-complementary hairpin-type moleculedoubled back on itself to form a duplex, the two strands (orduplex-forming regions of a single strand) are complementary RNA strandsthat base pair in Watson-Crick fashion.

Once introduced to a system, the compounds of the invention may elicitthe action of one or more enzymes or structural proteins to effectcleavage or other modification of the target nucleic acid or may workvia occupancy-based mechanisms. In general, nucleic acids (includingoligonucleotides) may be described as “DNA-like” (i.e., generally havingone or more 2′-deoxy sugars and, generally, T rather than U bases) or“RNA-like” (i.e., generally having one or more 2′-hydroxyl or2′-modified sugars and, generally U rather than T bases). Nucleic acidhelices can adopt more than one type of structure, most commonly the A-and B-forms. It is believed that, in general, oligonucleotides whichhave B-form-like structure are “DNA-like” and those which haveA-formlike structure are “RNA-like.” In some (chimeric) embodiments, anantisense compound may contain both A- and B-form regions.

In another embodiment, the desired oligonucleotides or antisensecompounds, comprise at least one of: antisense RNA, antisense DNA,chimeric antisense oligonucleotides, antisense oligonucleotidescomprising modified linkages, interference RNA (RNAi), short interferingRNA (siRNA); a micro, interfering RNA (miRNA); a small, temporal RNA(stRNA); or a short, hairpin RNA (shRNA); small RNA-induced geneactivation (RNAa); small activating RNAs (saRNAs), or combinationsthereof.

dsRNA can also activate gene expression, a mechanism that has beentermed “small RNA-induced gene activation” or RNAa. dsRNAs targetinggene promoters induce potent transcriptional activation of associatedgenes. RNAa was demonstrated in human cells using synthetic dsRNAs,termed “small activating RNAs” (saRNAs).

Small double-stranded RNA (dsRNA), such as small interfering RNA (siRNA)and microRNA (miRNA), have been found to be the trigger of anevolutionary conserved mechanism known as RNA interference (RNAi). RNAiinvariably leads to gene silencing. However, in instances described indetail in the examples section which follows, oligonucleotides are shownto increase the expression and/or function of the Reprogramming factorpolynucleotides and encoded products thereof. dsRNAs may also act assmall activating RNAs (saRNA). Without wishing to be bound by theory, bytargeting sequences in gene promoters, saRNAs would induce target geneexpression in a phenomenon referred to as dsRNA-induced transcriptionalactivation (RNAa).

In a further embodiment, the “preferred target segments” identifiedherein may be employed in a screen for additional compounds thatmodulate the expression of a Reprogramming factor polynucleotide.“Modulators” are those compounds that decrease or increase theexpression of a nucleic acid molecule encoding a Reprogramming factorand which comprise at least a 5-nucleotide portion that is complementaryto a preferred target segment. The screening method comprises the stepsof contacting a preferred target segment of a nucleic acid moleculeencoding sense or natural antisense polynucleotides of a Reprogrammingfactor with one or more candidate modulators, and selecting for one ormore candidate modulators which decrease or increase the expression of anucleic acid molecule encoding a Reprogramming factor polynucleotide,e.g. SEQ ID NOS: 7 to 17. Once it is shown that the candidate modulatoror modulators are capable of modulating (e.g. either decreasing orincreasing) the expression of a nucleic acid molecule encoding aReprogramming factor polynucleotide, the modulator may then be employedin further investigative studies of the function of a Reprogrammingfactor polynucleotide, or for use as a research, diagnostic, ortherapeutic agent in accordance with the present invention.

Targeting the natural antisense sequence modulates the function of thetarget gene. For example, the Reprogramming factor (e.g. accessionnumbers NM_(—)1003106, NM_(—)004235, NM_(—)002701). In a preferredembodiment, the target is an antisense polynucleotide of theReprogramming factor. In a preferred embodiment, an antisenseoligonucleotide targets sense and/or natural antisense sequences of aReprogramming factor polynucleotide (e.g. accession numbersNM_(—)003106, NM_(—)004235, NM_(—)002701), variants, alleles, isoforms,homologs, mutants, derivatives, fragments and complementary sequencesthereto. Preferably the oligonucleotide is an antisense molecule and thetargets include coding and noncoding regions of antisense and/or senseReprogramming factor polynucleotides.

The preferred target segments of the present invention may be also becombined with their respective complementary antisense compounds of thepresent invention to form stabilized double-stranded (duplexed)oligonucleotides.

Such double stranded oligonucleotide moieties have been shown in the artto modulate target expression and regulate translation as well as RNAprocessing via an antisense mechanism. Moreover, the double-strandedmoieties may be subject to chemical modifications. For example, suchdouble-stranded moieties have been shown to inhibit the target by theclassical hybridization of antisense strand of the duplex to the target,thereby triggering enzymatic degradation of the target.

In a preferred embodiment, an antisense oligonucleotide targetsReprogramming factor polynucleotides (e.g. accession numbersNM_(—)003106, NM_(—)004235, NM_(—)002701), variants, alleles, isoforms,homologs, mutants, derivatives, fragments and complementary sequencesthereto. Preferably the oligonucleotide is an antisense molecule.

In accordance with embodiments of the invention, the target nucleic acidmolecule is not limited to Reprogramming factor alone but extends to anyof the isoforms, receptors, homologs and the like of a Reprogrammingfactor molecule.

In another embodiment, an oligonucleotide targets a natural antisensesequence of a Reprogramming factor polynucleotide, for example,polynucleotides set forth as SEQ ID NO: 4 to 6, and any variants,alleles, homologs, mutants, derivatives, fragments and complementarysequences thereto. Examples of antisense oligonucleotides are set forthas SEQ ID NOS: 7 to 17.

In one embodiment, the oligonucleotides are complementary to or bind tonucleic acid sequences of a Reprogramming factor antisense, includingwithout limitation noncoding sense and/or antisense sequences associatedwith a Reprogramming factor polynucleotide and modulate expressionand/or function of a Reprogramming factor molecule.

In another embodiment, the oligonucleotides are complementary to or bindto nucleic acid sequences of a Reprogramming factor natural antisense,set forth as SEQ ID NO: 4 to 6 and modulate expression and/or functionof a Reprogramming factor molecule.

In a embodiment, oligonucleotides comprise sequences of at least 5consecutive nucleotides of SEQ ID NOS: 7 to 17 and modulate expressionand/or function of a Reprogramming factor molecule.

The polynucleotide targets comprise Reprogramming factor, includingfamily members thereof, variants of a Reprogramming factor; mutants of aReprogramming factor, including SNPs; noncoding sequences of aReprogramming factor; alleles of a Reprogramming factor; speciesvariants, fragments and the like. Preferably the oligonucleotide is anantisense molecule.

In another embodiment, the oligonucleotide targeting Reprogrammingfactor polynucleotides, comprise: antisense RNA, interference RNA(RNAi), short interfering RNA (siRNA); micro interfering RNA (miRNA); asmall, temporal RNA (stRNA); or a short, hairpin RNA (shRNA); smallRNA-induced gene activation (RNAa); or, small activating RNA (saRNA).

In another embodiment, targeting of a Reprogramming factorpolynucleotide, e.g. SEQ ID NO: 4 to 6 modulate the expression orfunction of these targets. In one embodiment, expression or function isup-regulated as compared to a control. In another preferred embodiment,expression or function is down-regulated as compared to a control.

In another embodiment, antisense compounds comprise sequences set forthas SEQ ID NOS: 7 to 17. These oligonucleotides can comprise one or moremodified nucleotides, shorter or longer fragments, modified bonds andthe like.

In another embodiment, SEQ ID NOS: 7 to 17 comprise one or more LNAnucleotides.

Table 1 shows exemplary antisense oligonucleotides useful in the methodsof the invention.

Antisense Sequence Sequence ID Name Sequence SEQ ID NO: 7 CUR-0404rArUrArArUrArArArUrGrGrArArCrGrUrGrGrCrUrGrGrUrArGrArU SEQ ID NO: 8CUR-0406 rCrUrGrArGrUrUrUrCrCrArGrUrGrGrGrUrArUrArUrUrUrArGrUrGSEQ ID NO: 9 CUR-0933 T*G*A*G*T*G*G*T*C*A*G*T*G*T*T*T*C*T*TSEQ ID NO: 10 CUR-0931 G*T*G*T*C*T*T*T*G*T*A*C*T*T*G*C*T*C*C*C*TSEQ ID NO: 11 CUR-0930 C*C*C*T*T*T*A*C*T*C*T*C*T*T*C*T*C*T*C*T*CSEQ ID NO: 12 CUR-0932 T*T*G*C*T*A*C*T*T*G*T*T*G*T*C*T*G*A*GSEQ ID NO: 13 CUR-1139 G*C*C*A*T*C*A*T*T*G*T*A*C*T*C*C*A*C*TSEQ ID NO: 14 CUR-1140 A*G*T*T*G*G*G*T*G*T*G*G*T*G*G*C*T*C*ASEQ ID NO: 15 CUR-1141 T*G*G*T*C*C*C*A*G*C*C*A*C*T*T*A*G*G*A*GSEQ ID NO: 16 CUR-1142 G*G*C*G*G*G*A*G*G*A*T*T*T*C*T*T*G*A*G*G*ASEQ ID NO: 17 CUR-1143 A*T*G*N*A*G*G*T*G*T*G*G*A*G*T*G*A*T*T*C

The modulation of a desired target nucleic acid can be carried out inseveral ways known in the art. For example, antisense oligonucleotides,siRNA etc. Enzymatic nucleic acid molecules (e.g., ribozymes) arenucleic acid molecules capable of catalyzing one or more of a variety ofreactions, including the ability to repeatedly cleave other separatenucleic acid molecules in a nucleotide base sequence-specific manner.Such enzymatic nucleic acid molecules can be used, for example, totarget virtually any RNA transcript.

Because of their sequence-specificity, trans-cleaving enzymatic nucleicacid molecules show promise as therapeutic agents for human disease.Enzymatic nucleic acid molecules can be designed to cleave specific RNAtargets within the background of cellular RNA. Such a cleavage eventrenders the mRNA non-functional and abrogates protein expression fromthat RNA. In this manner, synthesis of a protein associated with adisease state can be selectively inhibited.

In general, enzymatic nucleic acids with RNA cleaving activity act byfirst binding to a target RNA. Such binding occurs through the targetbinding portion of a enzymatic nucleic acid which is held in closeproximity to an enzymatic portion of the molecule that acts to cleavethe target RNA. Thus, the enzymatic nucleic acid first recognizes andthen binds a target RNA through complementary base pairing, and oncebound to the correct site, acts enzymatically to cut the target RNA.Strategic cleavage of such a target RNA will destroy its ability todirect synthesis of an encoded protein. After an enzymatic nucleic acidhas bound and cleaved its RNA target, it is released from that RNA tosearch for another target and can repeatedly bind and cleave newtargets.

Several approaches such as in vitro selection (evolution) strategieshave been used to evolve new nucleic acid catalysts capable ofcatalyzing a variety of reactions, such as cleavage and ligation ofphosphodiester linkages and amide linkages.

The development of ribozymes that are optimal for catalytic activitywould contribute significantly to any strategy that employs RNA-cleavingribozymes for the purpose of regulating gene expression. The hammerheadribozyme, for example, functions with a catalytic rate (kcat) of about 1min-1 in the presence of saturating (10 mM) concentrations of Mg2+cofactor. An artificial “RNA ligase” ribozyme has been shown to catalyzethe corresponding self-modification reaction with a rate of about 100min-1. In addition, it is known that certain modified hammerheadribozymes that have substrate binding arms made of DNA catalyze RNAcleavage with multiple turn-over rates that approach 100 min-1. Finally,replacement of a specific residue within the catalytic core of thehammerhead with certain nucleotide analogues gives modified ribozymesthat show as much as a 10-fold improvement in catalytic rate. Thesefindings demonstrate that ribozymes can promote chemical transformationswith catalytic rates that are significantly greater than those displayedin vitro by most natural self-cleaving ribozymes. It is then possiblethat the structures of certain selfcleaving ribozymes may be optimizedto give maximal catalytic activity, or that entirely new RNA motifs canbe made that display significantly faster rates for RNA phosphodiestercleavage.

Intermolecular cleavage of an RNA substrate by an RNA catalyst that fitsthe “hammerhead” model was first shown in 1987. The RNA catalyst wasrecovered and reacted with multiple RNA molecules, demonstrating that itwas truly catalytic.

Catalytic RNAs designed based on the “hammerhead” motif have been usedto cleave specific target sequences by making appropriate base changesin the catalytic RNA to maintain necessary base pairing with the targetsequences. This has allowed use of the catalytic RNA to cleave specifictarget sequences and indicates that catalytic RNAs designed according tothe “hammerhead” model may possibly cleave specific substrate RNAs invivo.

RNA interference (RNAi) has become a powerful tool for modulating geneexpression in mammals and mammalian cells. This approach requires thedelivery of small interfering RNA (siRNA) either as RNA itself or asDNA, using an expression plasmid or virus and the coding sequence forsmall hairpin RNAs that are processed to siRNAs. This system enablesefficient transport of the pre-siRNAs to the cytoplasm where they areactive and permit the use of regulated and tissue specific promoters forgene expression.

In one embodiment, an oligonucleotide or antisense compound comprises anoligomer or polymer of ribonucleic acid (RNA) and/or deoxyribonucleicacid (DNA), or a mimetic, chimera, analog or homolog thereof. This termincludes oligonucleotides composed of naturally occurring nucleotides,sugars and covalent internucleoside (backbone) linkages as well asoligonucleotides having non-naturally occurring portions which functionsimilarly. Such modified or substituted oligonucleotides are oftendesired over native forms because of desirable properties such as, forexample, enhanced cellular uptake, enhanced affinity for a targetnucleic acid and increased stability in the presence of nucleases.

According to the present invention, the oligonucleotides or “antisensecompounds” include antisense oligonucleotides (e.g. RNA, DNA, mimetic,chimera, analog or homolog thereof), ribozymes, external guide sequence(EGS) oligonucleotides, siRNA compounds, single- or double-stranded RNAinterference (RNAi) compounds such as siRNA compounds, saRNA, aRNA, andother oligomeric compounds which hybridize to at least a portion of thetarget nucleic acid and modulate its function. As such, they may be DNA,RNA, DNA-like, RNA-like, or mixtures thereof, or may be mimetics of oneor more of these. These compounds may be single-stranded,double-stranded, circular or hairpin oligomeric compounds and maycontain structural elements such as internal or terminal bulges,mismatches or loops. Antisense compounds are routinely prepared linearlybut can be joined or otherwise prepared to be circular and/or branched.Antisense compounds can include constructs such as, for example, twostrands hybridized to form a wholly or partially double-strandedcompound or a single strand with sufficient self-complementarity toallow for hybridization and formation of a fully or partiallydouble-stranded compound. The two strands can be linked internallyleaving free 3′ or 5′ termini or can be linked to form a continuoushairpin structure or loop. The hairpin structure may contain an overhangon either the 5′ or 3′ terminus producing an extension of singlestranded character. The double stranded compounds optionally can includeoverhangs on the ends. Further modifications can include conjugategroups attached to one of the termini, selected nucleotide positions,sugar positions or to one of the internucleoside linkages.Alternatively, the two strands can be linked via a non-nucleic acidmoiety or linker group. When formed from only one strand, dsRNA can takethe form of a self-complementary hairpin-type molecule that doubles backon itself to form a duplex. Thus, the dsRNAs can be fully or partiallydouble stranded. Specific modulation of gene expression can be achievedby stable expression of dsRNA hairpins in transgenic cell lines. Whenformed from two strands, or a single strand that takes the form of aself-complementary hairpin-type molecule doubled back on itself to forma duplex, the two strands (or duplex-forming regions of a single strand)are complementary RNA strands that base pair in Watson-Crick fashion.

Once introduced to a system, the compounds of the invention may elicitthe action of one or more enzymes or structural proteins to effectcleavage or other modification of the target nucleic acid or may workvia occupancy-based mechanisms. In general, nucleic acids (includingoligonucleotides) may be described as “DNA-like” (i.e., generally havingone or more 2′-deoxy sugars and, generally, T rather than U bases) or“RNA-like” (i.e., generally having one or more 2′-hydroxyl or2′-modified sugars and, generally U rather than T bases). Nucleic acidhelices can adopt more than one type of structure, most commonly the A-and B-forms. It is believed that, in general, oligonucleotides whichhave B-form-like structure are “DNA-like” and those which haveA-formlike structure are “RNA-like.” In some (chimeric) embodiments, anantisense compound may contain both A- and B-form regions.

The antisense compounds in accordance with this invention can comprisean antisense portion from about 5 to about 80 nucleotides (i.e. fromabout 5 to about 80 linked nucleosides) in length. This refers to thelength of the antisense strand or portion of the antisense compound. Inother words, a single-stranded antisense compound of the inventioncomprises from 5 to about 80 nucleotides, and a double-strandedantisense compound of the invention (such as a dsRNA, for example)comprises a sense and an antisense strand or portion of 5 to about 80nucleotides in length. One of ordinary skill in the art will appreciatethat this comprehends antisense portions of 5, 6, 7,8, 9, 10, 11, 12,13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48,49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66,67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 nucleotides inlength, or any range therewithin.

In one embodiment, the antisense compounds of the invention haveantisense portions of 10 to 50 nucleotides in length. One havingordinary skill in the art will appreciate that this embodiesoligonucleotides having antisense portions of 10, 11, 12, 13, 14, 15,16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33,34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50nucleotides in length, or any range therewithin. In some embodiments,the oligonucleotides are 15 nucleotides in length.

In one embodiment, the antisense or oligonucleotide compounds of theinvention have antisense portions of 12 or 13 to 30 nucleotides inlength. One having ordinary skill in the art will appreciate that thisembodies antisense compounds having antisense portions of 12, 13, 14,15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30nucleotides in length, or any range therewithin.

In another embodiment, the oligomeric compounds of the present inventionalso include variants in which a different base is present at one ormore of the nucleotide positions in the compound. For example, if thefirst nucleotide is an adenosine, variants may be produced which containthymidine, guanosine or cytidine at this position. This may be done atany of the positions of the antisense or dsRNA compounds. Thesecompounds are then tested using the methods described herein todetermine their ability to inhibit expression of a target nucleic acid.

In some embodiments, homology, sequence identity or complementarity,between the antisense compound and target is from about 40% to about60%. In some embodiments, homology, sequence identity orcomplementarity, is from about 60% to about 70%. In some embodiments,homology, sequence identity or complementarity, is from about 70% toabout 80%. In some embodiments, homology, sequence identity orcomplementarity, is from about 80% to about 90%. In some embodiments,homology, sequence identity or complementarity, is about 90%, about 92%,about 94%, about 95%, about 96%, about 97%, about 98%, about 99% orabout 100%.

In another embodiment, the antisense oligonucleotides, such as forexample, nucleic acid molecules set forth in SEQ ID NOS: 4 to 17comprise one or more substitutions or modifications. In one embodiment,the nucleotides are substituted with locked nucleic acids (LNA).

In another embodiment, the oligonucleotides target one or more regionsof the nucleic acid molecules sense and/or antisense of coding and/ornon-coding sequences associated with Reprogramming factor and thesequences set forth as SEQ ID NOS: 1 to 3 and 4 to 6. Theoligonucleotides are also targeted to overlapping regions of SEQ ID NOS:1 to 3 and 4 to 6.

Certain oligonucleotides of this invention are chimericoligonucleotides. “Chimeric oligonucleotides” or “chimeras,” in thecontext of this invention, are oligonucleotides which contain two ormore chemically distinct regions, each made up of at least onenucleotide. These oligonucleotides typically contain at least one regionof modified nucleotides that confers one or more beneficial properties(such as, for example, increased nuclease resistance, increased uptakeinto cells, increased binding affinity for the target) and a region thatis a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNAhybrids. By way of example, RNase H is a cellular endonuclease whichcleaves the RNA strand of an RNA:DNA duplex. Activation of RNase H,therefore, results in cleavage of the RNA target, thereby greatlyenhancing the efficiency of antisense modulation of gene expression.Consequently, comparable results can often be obtained with shorteroligonucleotides when chimeric oligonucleotides are used, compared tophosphorothioate deoxyoligonucleotides hybridizing to the same targetregion. Cleavage of the RNA target can be routinely detected by gelelectrophoresis and, if necessary, associated nucleic acid hybridizationtechniques known in the art. In one preferred embodiment, a chimericoligonucleotide comprises at least one region modified to increasetarget binding affinity, and, usually, a region that acts as a substratefor RNAse H Affinity of an oligonucleotide for its target (in this case,a nucleic acid encoding ras) is routinely determined by measuring the Tmof an oligonucleotide/target pair, which is the temperature at which theoligonucleotide and target dissociate; dissociation is detectedspectrophotometrically. The higher the Tm, the greater is the affinityof the oligonucleotide for the target.

Chimeric antisense compounds of the invention may be formed as compositestructures of two or more oligonucleotides, modified oligonucleotides,oligonucleosides and/or oligonucleotides mimetics as described above.Such; compounds have also been referred to in the art as hybrids orgapmers. Representative United States patents that teach the preparationof such hybrid structures comprise, but are not limited to, U.S. Pat.Nos. 5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711;5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and 5,700,922,each of which is herein incorporated by reference.

In another embodiment, the region of the oligonucleotide which ismodified comprises at least one nucleotide modified at the 2′ positionof the sugar, most preferably a 2′-Oalkyl, 2′-O-alkyl-O-alkyl or2′-fluoro-modified nucleotide. In other preferred embodiments, RNAmodifications include 2′-fluoro, 2′-amino and 2′ O-methyl modificationson the ribose of pyrimidines, abasic residues or an inverted base at the3′ end of the RNA. Such modifications are routinely incorporated intooligonucleotides and these oligonucleotides have been shown to have ahigher Tm (i.e., higher target binding affinity) than;2′-deoxyoligonucleotides against a given target. The effect of suchincreased affinity is to greatly enhance RNAi oligonucleotide inhibitionof gene expression. RNAse H is a cellular endonuclease that cleaves theRNA strand of RNA:DNA duplexes; activation of this enzyme thereforeresults in cleavage of the RNA target, and thus can greatly enhance theefficiency of RNAi inhibition. Cleavage of the RNA target can beroutinely demonstrated by gel electrophoresis. In another preferredembodiment, the chimeric oligonucleotide is also modified to enhancenuclease resistance. Cells contain a variety of exo- and endo-nucleaseswhich can degrade nucleic acids. A number of nucleotide and nucleosidemodifications have been shown to make the oligonucleotide into whichthey are incorporated more resistant to nuclease digestion than thenative oligodeoxynucleotide. Nuclease resistance is routinely measuredby incubating oligonucleotides with cellular extracts or isolatednuclease solutions and measuring the extent of intact oligonucleotideremaining over time, usually by gel electrophoresis. Oligonucleotideswhich have been modified to enhance their nuclease resistance surviveintact for a longer time than unmodified oligonucleotides. A variety ofoligonucleotide modifications have been demonstrated to enhance orconfer nuclease resistance. Oligonucleotides which contain at least onephosphorothioate modification are presently more preferred. In somecases, oligonucleotide modifications which enhance target bindingaffinity are also, independently, able to enhance nuclease resistance.Some desirable modifications can be found in De Mesmaeker et al. (1995)Acc. Chem. Res., 28:366-374.

Specific examples of some preferred oligonucleotides envisioned for thisinvention include those comprising modified backbones, for example,phosphorothioates, phosphotriesters, methyl phosphonates, short chainalkyl or cycloalkyl intersugar linkages or short chain heteroatomic orheterocyclic intersugar linkages. Most preferred are oligonucleotideswith phosphorothioate backbones and those with heteroatom backbones,particularly CH2—NH—O—CH2, CH,—N(CH3)-O—CH2 [known as amethylene(methylimino) or MMI backbone], CH2-O—N(CH3)-2,CH2-N(CH3)-N(CH3)-CH2 and O—N(CH3)-CH2-CH2 backbones, wherein the nativephosphodiester backbone is represented as O—P—O—CH,). The amidebackbones disclosed by De Mesmaeker et al. (1995) Acc. Chem. Res.28:366-374 are also preferred. Also preferred are oligonucleotideshaving morpholino backbone structures (Summerton and Weller, U.S. Pat.No. 5,034,506). In other preferred embodiments, such as the peptidenucleic acid (PNA) backbone, the phosphodiester backbone of theoligonucleotide is replaced with a polyamide backbone, the nucleotidesbeing bound directly or indirectly to the aza nitrogen atoms of thepolyamide backbone (Nielsen et al. (1991) Science 254, 1497).Oligonucleotides may also comprise one or more substituted sugarmoieties. Preferred oligonucleotides comprise one of the following atthe 2′ position: OH, SH, SCH3, F, OCN, OCH3 OCH3, OCH3O(CH2)n CH3,O(CH2)n NH2 or O(CH2)n CH3 where n is from 1 to about 10; C1 to C10lower alkyl, alkoxyalkoxy, substituted lower alkyl, alkaryl or aralkyl;Cl; Br; CN; CF3 ; OCF3; O—, S—, or N-alkyl;O—, S—, or N-alkenyl; SOCH3;SO2 CH3; ONO2; NO2; N3; NH2; heterocycloalkyl; heterocycloalkaryl;aminoalkylamino; polyalkylamino; substituted silyl; an RNA cleavinggroup; 0a reporter group; an intercalator; a group for improving thepharmacokinetic properties of an oligonucleotide; or a group forimproving the pharmacodynamic properties of an oligonucleotide and othersubstituents having similar properties. A preferred modificationincludes 2′-methoxyethoxy [2′-O—CH2 CH2 OCH3, also known as2′-O-(2-methoxyethyl)] (Martin et al., (1995) Helv. Chim. Acta, 78,486). Other preferred modifications include 2′-methoxy (2′-O—CH3),2′-propoxy (2′-OCH2 CH2CH3) and 2′-fluoro (2′-F). Similar modificationsmay also be made at other positions on the oligonucleotide, particularlythe 3′ position of the sugar on the 3′ terminal nucleotide and the 5′position of 5′ terminal nucleotide. Oligonucleotides may also have sugarmimetics such as cyclobutyls in place of the pentofuranosyl group.

Oligonucleotides may also include, additionally or alternatively,nucleobase (often referred to in the art simply as “base”) modificationsor substitutions. As used herein, “unmodified” or “natural” nucleotidesinclude adenine (A), guanine (G), thymine (T), cytosine (C) and uracil(U). Modified nucleotides include nucleotides found only infrequently ortransiently in natural nucleic acids, e.g., hypoxanthine,6-methyladenine, 5-Me pyrimidines, particularly 5-methylcytosine (alsoreferred to as 5-methyl-2′ deoxycytosine and often referred to in theart as 5-Me-C), 5-hydroxymethylcytosine (HMC), glycosyl HMC andgentobiosyl HMC, as well as synthetic nucleotides, e.g., 2-aminoadenine,2-(methylamino)adenine, 2-(imidazolylalkyl)adenine,2-(aminoalklyamino)adenine or other heterosubstituted alkyladenines,2-thiouracil, 2-thiothymine, 5-bromouracil, 5-hydroxymethyluracil,8-azaguanine, 7-deazaguanine, N6 (6-aminohexyl)adenine and2,6-diaminopurine. (Kornberg, A., DNA Replication, W. H. Freeman & Co.,San Francisco, 1980, pp 75-77; Gebeyehu, G., (1987) et al. Nucl. AcidsRes. 15:4513). A “universal” base known in the art, e.g., inosine, maybe included. 5-Me-C substitutions have been shown to increase nucleicacid duplex stability by 0.6-1.2° C. (Sanghvi, Y. S., in Crooke, S. T.and Lebleu, B., eds., Antisense Research and Applications, CRC Press,Boca Raton, 1993, pp. 276-278) and are presently preferred basesubstitutions.

Another modification of the oligonucleotides of the invention involveschemically linking to the oligonucleotide one or more moieties orconjugates which enhance the activity or cellular uptake of theoligonucleotide. Such moieties include but are not limited to lipidmoieties such as a cholesterol moiety, a cholesteryl moiety, athioether, e.g., hexyl-S-tritylthiol, a thiocholesterol, an aliphaticchain, e.g., dodecandiol or undecyl residues, a phospholipid, e.g.,di-hexadecyl-rac-glycerol or triethylammonium1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or apolyethylene glycol chain, or adamantane acetic acid . Oligonucleotidescomprising lipophilic moieties, and methods for preparing sucholigonucleotides are known in the art, for example, U.S. Pat. Nos.5,138,045, 5,218,105 and 5,459,255.

It is not necessary for all positions in a given oligonucleotide to beuniformly modified, and in fact more than one of the aforementionedmodifications may be incorporated in a single oligonucleotide or even atwithin a single nucleoside within an oligonucleotide. The presentinvention also includes oligonucleotides which are chimericoligonucleotides as hereinbefore defined.

In another embodiment, the nucleic acid molecule of the presentinvention is conjugated with another moiety including but not limited toabasic nucleotides, polyether, polyamine, polyamides, peptides,carbohydrates, lipid, or polyhydrocarbon compounds. Those skilled in theart will recognize that these molecules can be linked to one or more ofany nucleotides comprising the nucleic acid molecule at severalpositions on the sugar, base or phosphate group.

The oligonucleotides used in accordance with this invention may beconveniently and routinely made through the well-known technique ofsolid phase synthesis. Equipment for such synthesis is sold by severalvendors including Applied Biosystems. Any other means for such synthesismay also be employed; the actual synthesis of the oligonucleotides iswell within the talents of one of ordinary skill in the art. It is alsowell known to use similar techniques to prepare other oligonucleotidessuch as the phosphorothioates and alkylated derivatives. It is also wellknown to use similar techniques and commercially available modifiedamidites and controlled-pore glass (CPG) products such as biotin,fluorescein, acridine or psoralen-modified amidites and/or CPG(available from Glen Research, Sterling Va.) to synthesize fluorescentlylabeled, biotinylated or other modified oligonucleotides such ascholesterol-modified oligonucleotides.

In accordance with the invention, use of modifications such as the useof LNA monomers to enhance the potency, specificity and duration ofaction and broaden the routes of administration of oligonucleotidescomprised of current chemistries such as MOE, ANA, FANA, PS etc (Uhlman,et al. (2000) Current Opinions in Drug Discovery & Development Vol. 3 No2). This can be achieved by substituting some of the monomers in thecurrent oligonucleotides by LNA monomers. The LNA modifiedoligonucleotide may have a size similar to the parent compound or may belarger or preferably smaller. It is preferred that such LNA-modifiedoligonucleotides contain less than about 70%, more preferably less thanabout 60%, most preferably less than about 50% LNA monomers and thattheir sizes are between about 5 and 25 nucleotides, more preferablybetween about 12 and 20 nucleotides.

Modified oligonucleotide backbones comprise, but are not limited to,phosphorothioates, chiral phosphorothioates, phosphorodithioates,phosphotriesters, aminoalkylphosphotriesters, methyl and other alkylphosphonates comprising 3′alkylene phosphonates and chiral phosphonates,phosphinates, phosphoramidates comprising 3′-amino phosphoramidate andaminoalkylphosphoramidates, thionophosphoramidates,thionoalkylphosphonates, thionoalkylphosphotriesters, andboranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs ofthese, and those having inverted polarity wherein the adjacent pairs ofnucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Varioussalts, mixed salts and free acid forms are also included.

Representative United States patents that teach the preparation of theabove phosphorus containing linkages comprise, but are not limited to,U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196;5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131;5,399,676; 5,405,939; 5,453,496; 5,455, 233; 5,466,677; 5,476,925;5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799;5,587,361; and 5,625,050, each of which is herein incorporated byreference.

Modified oligonucleotide backbones that do not include a phosphorus atomtherein have backbones that are formed by short chain alkyl orcycloalkyl internucleoside linkages, mixed heteroatom and alkyl orcycloalkyl internucleoside linkages, or one or more short chainheteroatomic or heterocyclic internucleoside linkages. These comprisethose having morpholino linkages (formed in part from the sugar portionof a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; alkene containing backbones; sulfamatebackbones; methyleneimino and methylenehydrazino backbones; sulfonateand sulfonamide backbones; amide backbones; and others having mixed N,O, S and CH2 component parts.

Representative United States patents that teach the preparation of theabove oligonucleosides comprise, but are not limited to, U.S. Pat. Nos.5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677;5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240;5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360;5,677,437; and 5,677,439, each of which is herein incorporated byreference.

In other oligonucleotide mimetics, both the sugar and theinternucleoside linkage, i.e., the backbone, of the nucleotide units arereplaced with novel groups. The base units are maintained forhybridization with an appropriate nucleic acid target compound. One sucholigomeric compound, an oligonucleotide mimetic that has been shown tohave excellent hybridization properties, is referred to as a peptidenucleic acid (PNA). In PNA compounds, the sugar-backbone of anoligonucleotide is replaced with an amide containing backbone, inparticular an aminoethylglycine backbone. The nucleobases are retainedand are bound directly or indirectly to aza nitrogen atoms of the amideportion of the backbone. Representative United States patents that teachthe preparation of PNA compounds comprise, but are not limited to, U.S.Pat. Nos. 5,539,082; 5,714,331; and 5,719,262, each of which is hereinincorporated by reference . Further teaching of PNA compounds can befound in Nielsen, et al. (1991) Science 254, 1497-1500.

In another embodiment of the invention the oligonucleotides withphosphorothioate backbones and oligonucleosides with heteroatombackbones, and in particular —CH2-NH—O—CH2-, —CH2-N(CH3)-O—CH2-known asa methylene (methylimino) or MMI backbone, —CH2-O—N(CH3)-CH2-,—CH2N(CH3)-N(CH3)CH2- and —O—N(CH3)-CH2-CH2- wherein the nativephosphodiester backbone is represented as —O—P—O—CH2- of the abovereferenced U.S. Pat. No. 5,489,677, and the amide backbones of the abovereferenced U.S. Pat. No. 5,602,240. Also preferred are oligonucleotideshaving morpholino backbone structures of the above-referenced U.S. Pat.No. 5,034,506.

Modified oligonucleotides may also contain one or more substituted sugarmoieties. Preferred oligonucleotides comprise one of the following atthe 2′ position: OH; F; O—, S—, or N-alkyl; O—, S—, or N-alkenyl; O—,S—or N-alkynyl; or O alkyl-O-alkyl, wherein the alkyl, alkenyl andalkynyl may be substituted or unsubstituted C to CO alkyl or C2 to COalkenyl and alkynyl. Particularly preferred are O(CH2)n OmCH3,O(CH2)n,OCH3, O(CH2)nNH2, O(CH2)nCH3, O(CH2)nONH2, andO(CH2nON(CH2)nCH3)2 where n and m can be from 1 to about 10. Otherpreferred oligonucleotides comprise one of the following at the 2′position: C to CO, (lower alkyl, substituted lower alkyl, alkaryl,aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3,SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl,aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleavinggroup, a reporter group, an intercalator, a group for improving thepharmacokinetic properties of an oligonucleotide, or a group forimproving the pharmacodynamic properties of an oligonucleotide, andother substituents having similar properties. A preferred modificationcomprises 2′-methoxyethoxy (2′-O—CH2CH2OCH3, also known as2′-O-(2-methoxyethyl) or 2′-MOE) (Martin et al., (1995) Helv. Chim.Acta, 78, 486-504) i.e., an alkoxyalkoxy group. A further preferredmodification comprises 2′-dimethylaminooxyethoxy, i.e. , aO(CH2)2ON(CH3)2 group, also known as 2′-DMAOE, as described in examplesherein below, and 2′-dimethylaminoethoxyethoxy (also known in the art as2′-O-dimethylaminoethoxyethyl or 2′-DMAEOE), i.e.,2′-O—CH2-O—CH2-N(CH2)2.

Other modifications comprise 2′-methoxy (2′-OCH3), 2′-aminopropoxy(2′-OCH2CH2CH2NH2) and 2′-fluoro (2′-F). Similar modifications may alsobe made at other positions on the oligonucleotide, particularly the 3′position of the sugar on the 3′ terminal nucleotide or in 2′-5′ linkedoligonucleotides and the 5′ position of 5′ terminal nucleotide.Oligonucleotides may also have sugar mimetics such as cyclobutylmoieties in place of the pentofuranosyl sugar. Representative UnitedStates patents that teach the preparation of such modified sugarstructures comprise, but are not limited to, U.S. Pat. Nos. 4,981,957;5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786;5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909;5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and5,700,920, each of which is herein incorporated by reference.

Oligonucleotides may also comprise nucleobase (often referred to in theart simply as “base”) modifications or substitutions. As used herein,“unmodified” or “natural” nucleotides comprise the purine bases adenine(A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C)and uracil (U). Modified nucleotides comprise other synthetic andnatural nucleotides such as 5-methylcytosine (5-me-C), 5-hydroxymethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and otheralkyl derivatives of adenine and guanine, 2-propyl and other alkylderivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and2-thiocytosine, 5-halouracil and cytosine, 5-propynyl uracil andcytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudo-uracil),4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl andother 8-substituted adenines and guanines, 5-halo particularly 5-bromo,5-trifluoromethyl and other 5-substituted uracils and cytosines,7-methylquanine and 7-methyladenine, 8-azaguanine and 8-azaadenine,7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine.

Further, nucleotides comprise those disclosed in U.S. Pat. No.3,687,808, those disclosed in ‘The Concise Encyclopedia of PolymerScience And Engineering’, pages 858-859, Kroschwitz, J. I., ed. JohnWiley & Sons, 1990, those disclosed by Englisch et al., ‘AngewandleChemie, International Edition’, 1991, 30, page 613, and those disclosedby Sanghvi, Y. S., Chapter 15, ‘Antisense Research and Applications’,pages 289-302, Crooke, S. T. and Lebleu, B. ea., CRC Press, 1993.Certain of these nucleotides are particularly useful for increasing thebinding affinity of the oligomeric compounds of the invention. Thesecomprise 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and0-6 substituted purines, comprising 2-aminopropyladenine,5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutionshave been shown to increase nucleic acid duplex stability by 0.6-1.2° C.(Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., eds, ‘Antisense Researchand Applications’, CRC Press, Boca Raton, 1993, pp. 276-278) and arepresently preferred base substitutions, even more particularly whencombined with 2′-Omethoxyethyl sugar modifications.

Representative United States patents that teach the preparation of theabove noted modified nucleotides as well as other modified nucleotidescomprise, but are not limited to, U.S. Pat. No. 3,687,808, as well asU.S. Pat. Nos. 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066;5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711;5,552,540; 5,587,469; 5,596,091; 5,614,617; 5,750,692, and 5,681,941,each of which is herein incorporated by reference.

Another modification of the oligonucleotides of the invention involveschemically linking to the oligonucleotide one or more moieties orconjugates, which enhance the activity, cellular distribution, orcellular uptake of the oligonucleotide.

Such moieties comprise but are not limited to, lipid moieties such as acholesterol moiety, cholic acid, a thioether, e.g., hexyl-S-tritylthiol(Manoharan et al., (1992) Ann. N.Y. Acad. Sci., 660, 306-309; Manoharanet al., (1993) Bioorg. Med. Chem. Let., 3, 2765-2770), a thiocholesterol, an aliphatic chain, e.g., dodecandiol or undecyl residues , aphospholipid, e.g., di-hexadecyl-rac-glycerol or triethylammonium1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate, a polyamine or apolyethylene glycol chain, or adamantane acetic acid, a palmityl moiety, or an octadecylamine or hexylamino-carbonyl-t oxycholesterol moiety.

Representative United States patents that teach the preparation of sucholigonucleotides conjugates comprise, but are not limited to, U.S. Pat.Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730;5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124;5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718;5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737;4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830;5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022;5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098;5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667;5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371;5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, each of whichis herein incorporated by reference.

Drug discovery: The compounds of the present invention can also beapplied in the areas of drug discovery and target validation. Thepresent invention comprehends the use of the compounds and preferredtarget segments identified herein in drug discovery efforts to elucidaterelationships that exist between a Reprogramming factor polynucleotideand a disease state, phenotype, or condition. These methods includedetecting or modulating a Reprogramming factor polynucleotide comprisingcontacting a sample, tissue, cell, or organism with the compounds of thepresent invention, measuring the nucleic acid or protein level of aReprogramming factor polynucleotide and/or a related phenotypic orchemical endpoint at some time after treatment, and optionally comparingthe measured value to a non-treated sample or sample treated with afurther compound of the invention. These methods can also be performedin parallel or in combination with other experiments to determine thefunction of unknown genes for the process of target validation or todetermine the validity of a particular gene product as a target fortreatment or prevention of a particular disease, condition, orphenotype.

Assessing Up-Regulation or Inhibition of Gene Expression:

Transfer of an exogenous nucleic acid into a host cell or organism canbe assessed by directly detecting the presence of the nucleic acid inthe cell or organism. Such detection can be achieved by several methodswell known in the art. For example, the presence of the exogenousnucleic acid can be detected by Southern blot or by a polymerase chainreaction (PCR) technique using primers that specifically amplifynucleotide sequences associated with the nucleic acid. Expression of theexogenous nucleic acids can also be measured using conventional methodsincluding gene expression analysis. For instance, mRNA produced from anexogenous nucleic acid can be detected and quantified using a Northernblot and reverse transcription PCR (RT-PCR).

Expression of RNA from the exogenous nucleic acid can also be detectedby measuring an enzymatic activity or a reporter protein activity. Forexample, antisense modulatory activity can be measured indirectly as adecrease or increase in target nucleic acid expression as an indicationthat the exogenous nucleic acid is producing the effector RNA. Based onsequence conservation, primers can be designed and used to amplifycoding regions of the target genes. Initially, the most highly expressedcoding region from each gene can be used to build a model control gene,although any coding or non coding region can be used. Each control geneis assembled by inserting each coding region between a reporter codingregion and its poly(A) signal. These plasmids would produce an mRNA witha reporter gene in the upstream portion of the gene and a potential RNAitarget in the 3′ non-coding region. The effectiveness of individualantisense oligonucleotides would be assayed by modulation of thereporter gene. Reporter genes useful in the methods of the presentinvention include acetohydroxyacid synthase (AHAS), alkaline phosphatase(AP), beta galactosidase (LacZ), beta glucoronidase (GUS),chloramphenicol acetyltransferase (CAT), green fluorescent protein(GFP), red fluorescent protein (RFP), yellow fluorescent protein (YFP),cyan fluorescent protein (CFP), horseradish peroxidase (HRP), luciferase(Luc), nopaline synthase (NOS), octopine synthase (OCS), and derivativesthereof. Multiple selectable markers are available that conferresistance to ampicillin, bleomycin, chloramphenicol, gentamycin,hygromycin, kanamycin, lincomycin, methotrexate, phosphinothricin,puromycin, and tetracycline. Methods to determine modulation of areporter gene are well known in the art, and include, but are notlimited to, fluorometric methods (e.g. fluorescence spectroscopy,Fluorescence Activated Cell Sorting (FACS), fluorescence microscopy),antibiotic resistance determination.

Sox2, KLF4, and POU5F1 proteins and mRNA expression can be assayed usingmethods known to those of skill in the art and described elsewhereherein. For example, immunoassays such as the ELISA can be used tomeasure protein levels. Reprogramming factor antibodies for ELISAs areavailable commercially, e.g., from R&D Systems (Minneapolis, Minn.),Abcam, Cambridge, Mass.

In embodiments, Sox2, KLF4, and POU5F1 expression (e.g., mRNA orprotein) in a sample (e.g., cells or tissues in vivo or in vitro)treated using an antisense oligonucleotide of the invention is evaluatedby comparison with Reprogramming factor expression in a control sample.For example, expression of the protein or nucleic acid can be comparedusing methods known to those of skill in the art with that in amock-treated or untreated sample. Alternatively, comparison with asample treated with a control antisense oligonucleotide (e.g., onehaving an altered or different sequence) can be made depending on theinformation desired. In another embodiment, a difference in theexpression of the Reprogramming factor protein or nucleic acid in atreated vs. an untreated sample can be compared with the difference inexpression of a different nucleic acid (including any standard deemedappropriate by the researcher, e.g., a housekeeping gene) in a treatedsample vs. an untreated sample.

Observed differences can be expressed as desired, e.g., in the form of aratio or fraction, for use in a comparison with control. In embodiments,the level of a Reprogramming factor mRNA or protein, in a sample treatedwith an antisense oligonucleotide of the present invention, is increasedor decreased by about 1.25-fold to about 10-fold or more relative to anuntreated sample or a sample treated with a control nucleic acid. Inembodiments, the level of a Reprogramming factor mRNA or protein isincreased or decreased by at least about 1.25-fold, at least about1.3-fold, at least about 1.4-fold, at least about 1.5-fold, at leastabout 1.6-fold, at least about 1.7-fold, at least about 1.8-fold, atleast about 2-fold, at least about 2.5-fold, at least about 3-fold, atleast about 3.5-fold, at least about 4-fold, at least about 4.5-fold, atleast about 5-fold, at least about 5.5-fold, at least about 6-fold, atleast about 6.5-fold, at least about 7-fold, at least about 7.5-fold, atleast about 8-fold, at least about 8.5-fold, at least about 9-fold, atleast about 9.5-fold, or at least about 10-fold or more.

Kits, Research Reagents, Diagnostics, and Therapeutics

The compounds of the present invention can be utilized for diagnostics,therapeutics, and prophylaxis, and as research reagents and componentsof kits. Furthermore, antisense oligonucleotides, which are able toinhibit gene expression with exquisite specificity, are often used bythose of ordinary skill to elucidate the function of particular genes orto distinguish between functions of various members of a biologicalpathway.

For use in kits and diagnostics and in various biological systems, thecompounds of the present invention, either alone or in combination withother compounds or therapeutics, are useful as tools in differentialand/or combinatorial analyses to elucidate expression patterns of aportion or the entire complement of genes expressed within cells andtissues.

As used herein the term “biological system” or “system” is defined asany organism, cell, cell culture or tissue that expresses, or is madecompetent to express products of the Reprogramming factors. Theseinclude, but are not limited to, humans, transgenic animals, cells, cellcultures, tissues, xenografts, transplants and combinations thereof.

As one non limiting example, expression patterns within cells or tissuestreated with one or more antisense compounds are compared to controlcells or tissues not treated with antisense compounds and the patternsproduced are analyzed for differential levels of gene expression as theypertain, for example, to disease association, signaling pathway,cellular localization, expression level, size, structure or function ofthe genes examined. These analyses can be performed on stimulated orunstimulated cells and in the presence or absence of other compoundsthat affect expression patterns.

Examples of methods of gene expression analysis known in the art includeDNA arrays or microarrays (Brazma and Vilo, (2000) FEBS Lett., 480,17-24; Celis, et al., (2000) FEBS Lett., 480, 2-16), SAGE (serialanalysis of gene expression) (Madden, et al., (2000) Drug Discov. Today,5, 415-425), READS (restriction enzyme amplification of digested cDNAs)(Prashar and Weissman, (1999) Methods Enzymol., 303, 258-72), TOGA(total gene expression analysis) (Sutcliffe, et al., (2000) Proc. Natl.Acad. Sci. U.S.A., 97, 1976-81), protein arrays and proteomics (Celis,et al., (2000) FEBS Lett., 480, 2-16; Jungblut, et al., Electrophoresis,1999, 20, 2100-10), expressed sequence tag (EST) sequencing (Celis, etal., FEBS Left., 2000, 480, 2-16; Larsson, et al., J. Biotechnol., 2000,80, 143-57), subtractive RNA fingerprinting (SuRF) (Fuchs, et al.,(2000) Anal. Biochem. 286, 91-98; Larson, et al., (2000) Cytometry 41,203-208), subtractive cloning, differential display (DD) (Jurecic andBelmont, (2000) Curr. Opin. Microbiol. 3, 316-21), comparative genomichybridization (Carulli, et al., (1998) J. Cell Biochem. Suppl., 31,286-96), FISH (fluorescent in situ hybridization) techniques (Going andGusterson, (1999) Eur. J. Cancer, 35, 1895-904) and mass spectrometrymethods (To, Comb. (2000) Chem. High Throughput Screen, 3, 235-41).

The compounds of the invention are useful for research and diagnostics,because these compounds hybridize to nucleic acids encoding aReprogramming factor. For example, oligonucleotides that hybridize withsuch efficiency and under such conditions as disclosed herein as to beeffective Reprogramming factor modulators are effective primers orprobes under conditions favoring gene amplification or detection,respectively. These primers and probes are useful in methods requiringthe specific detection of nucleic acid molecules encoding aReprogramming factor and in the amplification of said nucleic acidmolecules for detection or for use in further studies of a Reprogrammingfactor. Hybridization of the antisense oligonucleotides, particularlythe primers and probes, of the invention with a nucleic acid encoding aReprogramming factor can be detected by means known in the art. Suchmeans may include conjugation of an enzyme to the oligonucleotide,radiolabeling of the oligonucleotide, or any other suitable detectionmeans. Kits using such detection means for detecting the level of aReprogramming factor in a sample may also be prepared.

The specificity and sensitivity of antisense are also harnessed by thoseof skill in the art for therapeutic uses. Antisense compounds have beenemployed as therapeutic moieties in the treatment of disease states inanimals, including humans. Antisense oligonucleotide drugs have beensafely and effectively administered to humans and numerous clinicaltrials are presently underway. It is thus established that antisensecompounds can be useful therapeutic modalities that can be configured tobe useful in treatment regimes for the treatment of cells, tissues andanimals, especially humans.

For therapeutics, an animal, preferably a human, suspected of having adisease or disorder which can be treated by modulating the expression ofa Reprogramming factor polynucleotide is treated by administeringantisense compounds in accordance with this invention. For example, inone non-limiting embodiment, the methods comprise the step ofadministering to the animal in need of treatment, a therapeuticallyeffective amount of a Reprogramming factor modulator. The Reprogrammingfactor modulators of the present invention effectively modulate theactivity of a Reprogramming factor or modulate the expression of aReprogramming factor protein. In one embodiment, the activity orexpression of a Reprogramming factor in an animal is inhibited by about10% as compared to a control. Preferably, the activity or expression ofa Reprogramming factor in an animal is inhibited by about 30%. Morepreferably, the activity or expression of a Reprogramming factor in ananimal is inhibited by 50% or more. Thus, the oligomeric compoundsmodulate expression of a Reprogramming factor mRNA by at least 10%, byat least 50%, by at least 25%, by at least 30%, by at least 40%, by atleast 50%, by at least 60%, by at least 70%, by at least 75%, by atleast 80%, by at least 85%, by at least 90%, by at least 95%, by atleast 98%, by at least 99%, or by 100% as compared to a control.

In one embodiment, the activity or expression of a Reprogramming factorand/or in an animal is increased by about 10% as compared to a control.Preferably, the activity or expression of a Reprogramming factor in ananimal is increased by about 30%. More preferably, the activity orexpression of a Reprogramming factor in an animal is increased by 50% ormore. Thus, the oligomeric compounds modulate expression of aReprogramming factor mRNA by at least 10%, by at least 50%, by at least25%, by at least 30%, by at least 40%, by at least 50%, by at least 60%,by at least 70%, by at least 75%, by at least 80%, by at least 85%, byat least 90%, by at least 95%, by at least 98%, by at least 99%, or by100% as compared to a control.

For example, the reduction of the expression of a Reprogramming factormay be measured in serum, blood,adipose tissue, liver or any other bodyfluid, tissue or organ of the animal. Preferably, the cells containedwithin said fluids, tissues or organs being analyzed contain a nucleicacid molecule encoding Reprogramming factor peptides and/or theReprogramming factor protein itself.

The compounds of the invention can be utilized in pharmaceuticalcompositions by adding an effective amount of a compound to a suitablepharmaceutically acceptable diluent or carrier. Use of the compounds andmethods of the invention may also be useful prophylactically.

Conjugates

Another modification of the oligonucleotides of the invention involveschemically linking to the oligonucleotide one or more moieties orconjugates that enhance the activity, cellular distribution or cellularuptake of the oligonucleotide. These moieties or conjugates can includeconjugate groups covalently bound to functional groups such as primaryor secondary hydroxyl groups. Conjugate groups of the invention includeintercalators, reporter molecules, polyamines, polyamides, polyethyleneglycols, polyethers, groups that enhance the pharmacodynamic propertiesof oligomers, and groups that enhance the pharmacokinetic properties ofoligomers. Typicalconjugate groups include cholesterols, lipids,phospholipids, biotin, phenazine, folate, phenanthridine, anthraquinone,acridine, fluoresceins, rhodamines, coumarins, and dyes. Groups thatenhance the pharmacodynamic properties, in the context of thisinvention, include groups that improve uptake, enhance resistance todegradation, and/or strengthen sequence-specific hybridization with thetarget nucleic acid. Groups that enhance the pharmacokinetic properties,in the context of this invention, include groups that improve uptake,distribution, metabolism or excretion of the compounds of the presentinvention. Representative conjugate groups are disclosed inInternational Patent Application No. PCT/US92/09196, filed Oct. 23,1992, and U.S. Pat. No. 6,287,860, which are incorporated herein byreference. Conjugate moieties include, but are not limited to, lipidmoieties such as a cholesterol moiety, cholic acid, a thioether, e.g.,hexyl-5-tritylthiol, a thiocholesterol, an aliphatic chain, e.g.,dodecandiol or undecyl residues, a phospholipid, e.g.,di-hexadecyl-rac-glycerol or triethylammonium1,2-di-O-hexadecyl-rac-glycero-3-Hphosphonate, a polyamine or apolyethylene glycol chain, or adamantane acetic acid, a palmityl moiety,or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety.Oligonucleotides of the invention may also be conjugated to active drugsubstances, for example, aspirin, warfarin, phenylbutazone, ibuprofen,suprofen, fenbufen, ketoprofen, (S)-(+)-pranoprofen, carprofen,dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinicacid, a benzothiadiazide, chlorothiazide, a diazepine, indomethicin, abarbiturate, a cephalosporin, a sulfa drug, an antidiabetic, anantibacterial or an antibiotic.

Representative United States patents that teach the preparation of sucholigonucleotides conjugates include, but are not limited to, U.S. Pat.Nos. 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730;5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124;5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718;5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737;4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830;5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022;5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098;5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667;5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371;5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941.

Formulations

The compounds of the invention may also be admixed, encapsulated,conjugated or otherwise associated with other molecules, moleculestructures or mixtures of compounds, as forexample, liposomes,receptor-targeted molecules, oral, rectal, topical or otherformulations, for assisting in uptake, distribution and/or absorption.Representative United States patents that teach the preparation of suchuptake, distribution and/or absorption-assisting formulations include,but are not limited to, U.S. Pat. Nos. 5,108,921; 5,354,844; 5,416,016;5,459,127; 5,521,291; 5,543,165; 5,547,932; 5,583,020; 5,591,721;4,426,330; 4,534,899; 5,013,556; 5,108,921; 5,213,804; 5,227,170;5,264,221; 5,356,633; 5,395,619; 5,416,016; 5,417,978; 5,462,854;5,469,854; 5,512,295; 5,527,528; 5,534,259; 5,543,152; 5,556,948;5,580,575; and 5,595,756, each of which is herein incorporated byreference.

Although, the antisense oligonucleotides do not need to be administeredin the context of a vector in order to modulate a target expressionand/or function, embodiments of the invention relates to expressionvector constructs for the expression of antisense oligonucleotides,comprising promoters, hybrid promoter gene sequences and possess astrong constitutive promoter activity, or a promoter activity which canbe induced in the desired case.

In an embodiment, invention practice involves administering at least oneof the foregoing antisense oligonucleotides with a suitable nucleic aciddelivery system. In one embodiment, that system includes a non-viralvector operably linked to the polynucleotide. Examples of such nonviralvectors include the oligonucleotide alone (e.g. any one or more of SEQID NOS: 7 to 17) or in combination with a suitable protein,polysaccharide or lipid formulation.

Additionally suitable nucleic acid delivery systems include viralvector, typically sequence from at least one of an adenovirus,adenovirus-associated virus (AAV), helper-dependent adenovirus,retrovirus, or hemagglutinatin virus of Japan-liposome (HVJ) complex.Preferably, the viral vector comprises a strong eukaryotic promoteroperably linked to the polynucleotide e.g., a cytomegalovirus (CMV)promoter.

Additionally preferred vectors include viral vectors, fusion proteinsand chemical conjugates. Retroviral vectors include Moloney murineleukemia viruses and HIV-based viruses. One preferred HIV-based viralvector comprises at least two vectors wherein the gag and pol genes arefrom an HIV genome and the env gene is from another virus. DNA viralvectors are preferred. These vectors include pox vectors such asorthopox or avipox vectors, herpesvirus vectors such as a herpes simplexI virus (HSV) vector [Geller, A. I. et al., (1995) J. Neurochem, 64:487; Lim, F., et al., in DNA Cloning: Mammalian Systems, D. Glover, Ed.(Oxford Univ. Press, Oxford England) (1995); Geller, A. I. et al.,(1993) Proc Natl. Acad. Sci.: U.S.A.:90 7603; Geller, A. I., et al.,(1990) Proc Natl. Acad. Sci USA: 87:1149], Adenovirus Vectors (LeGalLaSalle et al., Science, 259:988 (1993); Davidson, et al., (1993) Nat.Genet. 3: 219; Yang, et al., (1995) J. Virol. 69: 2004) andAdeno-associated Virus Vectors (Kaplitt, M. G., et al., (1994) Nat.Genet. 8:148).

The antisense compounds of the invention encompass any pharmaceuticallyacceptable salts, esters, or salts of such esters, or any other compoundwhich, upon administration to an animal, including a human, is capableof providing (directly or indirectly) the biologically active metaboliteor residue thereof.

The term “pharmaceutically acceptable salts” refers to physiologicallyand pharmaceutically acceptable salts of the compounds of the invention:i.e., salts that retain the desired biological activity of the parentcompound and do not impart undesired toxicological effects thereto. Foroligonucleotides, preferred examples of pharmaceutically acceptablesalts and their uses are further described in U.S. Pat. No. 6,287,860,which is incorporated herein by reference.

The present invention also includes pharmaceutical compositions andformulations that include the antisense compounds of the invention. Thepharmaceutical compositions of the present invention may be administeredin a number of ways depending upon whether local or systemic treatmentis desired and upon the area to be treated. Administration may betopical (including ophthalmic and to mucous membranes including vaginaland rectal delivery), pulmonary, e.g., by inhalation or insufflation ofpowders or aerosols, including by nebulizer; intratracheal, intranasal,epidermal and transdermal), oral or parenteral. Parenteraladministration includes intravenous, intraarterial, subcutaneous,intraperitoneal or intramuscular injection or infusion; or intracranial,e.g., intrathecal or intraventricular, administration.

For treating tissues in the central nervous system, administration canbe made by, e.g, injection or infusion into the cerebrospinal fluid.Administration of antisense RNA into cerebrospinal fluid is described,e.g., in U.S. Pat. App. Pub. No. 2007/0117772, “Methods for slowingfamilial ALS disease progression,” incorporated herein by reference inits entirety.

When it is intended that the antisense oligonucleotide of the presentinvention be administered to cells in the central nervous system,administration can be with one or more agents capable of promotingpenetration of the subject antisense oligonucleotide across theblood-brain barrier. Injection can be made, e.g., in the entorhinalcortex or hippocampus. Delivery of neurotrophic factors byadministration of an adenovirus vector to motor neurons in muscle tissueis described in, e.g., U.S. Pat. No. 6,632,427,“Adenoviral-vector-mediated gene transfer into medullary motor neurons,”incorporated herein by reference. Delivery of vectors directly to thebrain, e.g., the striatum, the thalamus, the hippocampus, or thesubstantia nigra, is known in the art and described, e.g., in U.S. Pat.No. 6,756,523, “Adenovirus vectors for the transfer of foreign genesinto cells of the central nervous system particularly in brain,”incorporated herein by reference. Administration can be rapid as byinjection or made over a period of time as by slow infusion oradministration of slow release formulations.

The subject antisense oligonucleotides can also be linked or conjugatedwith agents that provide desirable pharmaceutical or pharmacodynamicproperties. For example, the antisense oligonucleotide can be coupled toany substance, known in the art to promote penetration or transportacross the blood-brain barrier, such as an antibody to the transferrinreceptor, and administered by intravenous injection. The antisensecompound can be linked with a viral vector, for example, that makes theantisense compound more effective and/or increases the transport of theantisense compound across the blood-brain barrier. Osmotic blood brainbarrier disruption can also be accomplished by, e.g., infusion of sugarsincluding, but not limited to, meso erythritol, xylitol, D(+) galactose,D(+) lactose, D(+) xylose, dulcitol, myo-inositol, L(−) fructose, D(−)mannitol, D(+) glucose, D(+) arabinose, D(−) arabinose, cellobiose, D(+)maltose, D(+) raffinose, L(+) rhamnose, D(+) melibiose, D(−) ribose,adonitol, D(+) arabitol, L(−) arabitol, D(+) fucose, L(−) fucose, D(−)lyxose, L(+) lyxose, and L(−) lyxose, or amino acids including, but notlimited to, glutamine, lysine, arginine, asparagine, aspartic acid,cysteine, glutamic acid, glycine, histidine, leucine, methionine,phenylalanine, proline, serine, threonine, tyrosine, valine, andtaurine. Methods and materials for enhancing blood brain barrierpenetration are described, e.g., in U.S. Pat. No. 4,866,042, “Method forthe delivery of genetic material across the blood brain barrier,”6,294,520, “Material for passage through the blood-brain barrier,” andU.S. Pat. No. 6,936,589, “Parenteral delivery systems,” all incorporatedherein by reference in their entirety.

The subject antisense compounds may be admixed, encapsulated, conjugatedor otherwise associated with other molecules, molecule structures ormixtures of compounds, for example, liposomes, receptor-targetedmolecules, oral, rectal, topical or other formulations, for assisting inuptake, distribution and/or absorption. For example, cationic lipids maybe included in the formulation to facilitate oligonucleotide uptake. Onesuch composition shown to facilitate uptake is LIPOFECTIN (availablefrom GIBCO-BRL, Bethesda, Md.).

Oligonucleotides with at least one 2′-O-methoxyethyl modification arebelieved to be particularly useful for oral administration.Pharmaceutical compositions and formulations for topical administrationmay include transdermal patches, ointments, lotions, creams, gels,drops, suppositories, sprays, liquids and powders. Conventionalpharmaceutical carriers, aqueous, powder or oily bases, thickeners andthe like may be necessary or desirable. Coated condoms, gloves and thelike may also be useful.

The pharmaceutical formulations of the present invention, which mayconveniently be presented in unit dosage form, may be prepared accordingto conventional techniques well known in the pharmaceutical industry.Such techniques include the step of bringing into association the activeingredients with the pharmaceutical carrier(s) or excipient(s). Ingeneral, the formulations are prepared by uniformly and intimatelybringing into association the active ingredients with liquid carriers orfinely divided solid carriers or both, and then, if necessary, shapingthe product.

The compositions of the present invention may be formulated into any ofmany possible dosage forms such as, but not limited to, tablets,capsules, gel capsules, liquid syrups, soft gels, suppositories, andenemas. The compositions of the present invention may also be formulatedas suspensions in aqueous, non-aqueous or mixed media. Aqueoussuspensions may further contain substances that increase the viscosityof the suspension including, for example, sodium carboxymethylcellulose,sorbitol and/or dextran. The suspension may also contain stabilizers.

Pharmaceutical compositions of the present invention include, but arenot limited to, solutions, emulsions, foams and liposome-containingformulations. The pharmaceutical compositions and formulations of thepresent invention may comprise one or more penetration enhancers,carriers, excipients or other active or inactive ingredients.

Emulsions are typically heterogeneous systems of one liquid dispersed inanother in the form of droplets usually exceeding 0.1 μm in diameter.Emulsions may contain additional components in addition to the dispersedphases, and the active drug that may be present as a solution in eitherthe aqueous phase, oily phase or itself as a separate phase.Microemulsions are included as an embodiment of the present invention.Emulsions and their uses are well known in the art and are furtherdescribed in U.S. Pat. No. 6,287,860.

Formulations of the present invention include liposomal formulations. Asused in the present invention, the term “liposome” means a vesiclecomposed of amphiphilic lipids arranged in a spherical bilayer orbilayers. Liposomes are unilamellar or multilamellar vesicles which havea membrane formed from a lipophilic material and an aqueous interiorthat contains the composition to be delivered. Cationic liposomes arepositively charged liposomes that are believed to interact withnegatively charged DNA molecules to form a stable complex. Liposomesthat are pH-sensitive or negatively-charged are believed to entrap DNArather than complex with it. Both cationic and noncationic liposomeshave been used to deliver DNA to cells.

Liposomes also include “sterically stabilized” liposomes, a term which,as used herein, refers to liposomes comprising one or more specializedlipids. When incorporated into liposomes, these specialized lipidsresult in liposomes with enhanced circulation lifetimes relative toliposomeslacking such specialized lipids. Examples of stericallystabilized liposomes are those in which part of the vesicle-forminglipid portion of the liposome comprises one or more glycolipids or isderivatized with one or more hydrophilic polymers, such as apolyethylene glycol (PEG) moiety. Liposomes and their uses are furtherdescribed in U.S. Pat. No. 6,287,860.

The pharmaceutical formulations and compositions of the presentinvention may also include surfactants. The use of surfactants in drugproducts, formulations and in emulsions is well known in the art.Surfactants and their uses are further described in U.S. Pat. No.6,287,860, which is incorporated herein by reference.

In one embodiment, the present invention employs various penetrationenhancers to effect the efficient delivery of nucleic acids,particularly oligonucleotides. In addition to aiding the diffusion ofnon-lipophilic drugs across cell membranes, penetration enhancers alsoenhance the permeability of lipophilic drugs. Penetration enhancers maybe classified as belonging to one of five broad categories, i.e.,surfactants, fatty acids, bile salts, chelating agents, andnon-chelating nonsurfactants. Penetration enhancers and their uses arefurther described in U.S. Pat. No. 6,287,860, which is incorporatedherein by reference.

One of skill in the art will recognize that formulations are routinelydesigned according to their intended use, i.e. route of administration.

Preferred formulations for topical administration include those in whichthe oligonucleotides of the invention are in admixture with a topicaldelivery agent such as lipids, liposomes, fatty acids, fatty acidesters, steroids, chelating agents and surfactants. Preferred lipids andliposomes include neutral (e.g. dioleoyl-phosphatidyl DOPE ethanolamine,dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline)negative (e.g. dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g.dioleoyltetramethylaminopropyl DOTAP and dioleoyl-phosphatidylethanolamine DOTMA).

For topical or other administration, oligonucleotides of the inventionmay be encapsulated within liposomes or may form complexes thereto, inparticular to cationic liposomes. Alternatively, oligonucleotides may becomplexed to lipids, in particular to cationic lipids. Preferred fattyacids and esters, pharmaceutically acceptable salts thereof, and theiruses are further described in U.S. Pat. No. 6,287,860.

Compositions and formulations for oral administration include powders orgranules, microparticulates, nanoparticulates, suspensions or solutionsin water or non-aqueous media, capsules, gel capsules, sachets, tabletsor minitablets. Thickeners, flavoring agents, diluents, emulsifiers,dispersing aids or binders may be desirable. Preferred oral formulationsare those in which oligonucleotides of the invention are administered inconjunction with one or more penetration enhancers surfactants andchelators. Preferred surfactants include fatty acids and/or esters orsalts thereof, bile acids and/or salts thereof. Preferred bileacids/salts and fatty acids and their uses are further described in U.S.Pat. No. 6,287,860, which is incorporated herein by reference. Alsopreferred are combinations of penetration enhancers, for example, fattyacids/salts in combination with bile acids/salts. A particularlypreferred combination is the sodium salt of lauric acid, capric acid andUDCA. Further penetration enhancers include polyoxyethylene-9-laurylether, polyoxyethylene-20-cetyl ether. Oligonucleotides of the inventionmay be delivered orally, in granular form including sprayed driedparticles, or complexed to form micro or nanoparticles. Oligonucleotidecomplexing agents and their uses are further described in U.S. Pat. No.6,287,860, which is incorporated herein by reference.

Compositions and formulations for parenteral, intrathecal orintraventricular administration may include sterile aqueous solutionsthat may also contain buffers, diluents and other suitable additivessuch as, but not limited to, penetration enhancers, carrier compoundsand other pharmaceutically acceptable carriers or excipients.

Certain embodiments of the invention provide pharmaceutical compositionscontaining one or more oligomeric compounds and one or more otherchemotherapeutic agents that function by a non-antisense mechanism.Examples of such chemotherapeutic agents include but are not limited tocancer chemotherapeutic drugs such as daunorubicin, daunomycin,dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin,bleomycin, mafosfamide, ifosfamide, cytosine arabinoside,bischloroethyl-nitrosurea, busulfan, mitomycin C, actinomycin D,mithramycin, prednisone, hydroxyprogesterone, testosterone, tamoxifen,dacarbazine, procarbazine, hexamethylmelamine, pentamethylmelamine,mitoxantrone, amsacrine, chlorambucil, methylcyclohexylnitrosurea,nitrogen mustards, melphalan, cyclophosphamide, 6-mercaptopurine,6-thioguanine, cytarabine, 5-azacytidine, hydroxyurea, deoxycoformycin,4-hydroxyperoxycyclo-phosphoramide, 5-fluorouracil (5-FU),5-fluorodeoxyuridine (5-FUdR), methotrexate (MTX), colchicine, taxol,vincristine, vinblastine, etoposide (VP-16), trimetrexate, irinotecan,topotecan, gemcitabine, teniposide, cisplatin and diethylstilbestrol(DES). When used with the compounds of the invention, suchchemotherapeutic agents may be used individually (e.g., 5-FU andoligonucleotide), sequentially (e.g., 5-FU and oligonucleotide for aperiod of time followed by MTX and oligonucleotide), or in combinationwith one or more other such chemotherapeutic agents (e.g., 5-FU, MTX andoligonucleotide, or 5-FU, radiotherapy and oligonucleotide).Anti-inflammatory drugs, including but not limited to nonsteroidalanti-inflammatory drugs and corticosteroids, and antiviral drugs,including but not limited to ribivirin, vidarabine, acyclovir andganciclovir, may also be combined in compositions of the invention.Combinations of antisense compounds and other non-antisense drugs arealso within the scope of this invention. Two or more combined compoundsmay be used together or sequentially.

In another related embodiment, compositions of the invention may containone or more antisense compounds, particularly oligonucleotides, targetedto a first nucleic acid and one or more additional antisense compoundstargeted to a second nucleic acid target. For example, the first targetmay be a particular antisense sequence of a Reprogramming factor, andthe second target may be a region from another nucleotide sequence.Alternatively, compositions of the invention may contain two or moreantisense compounds targeted to different regions of the sameReprogramming factor nucleic acid target. Numerous examples of antisensecompounds are illustrated herein and others may be selected from amongsuitable compounds known in the art. Two or more combined compounds maybe used together or sequentially.

Dosing:

The formulation of therapeutic compositions and their subsequentadministration (dosing) is believed to be within the skill of those inthe art. Dosing is dependent on severity and responsiveness of thedisease state to be treated, with the course of treatment lasting fromseveral days to several months, or until a cure is effected or adiminution of the disease state is achieved. Optimal dosing schedulescan be calculated from measurements of drug accumulation in the body ofthe patient. Persons of ordinary skill can easily determine optimumdosages, dosing methodologies and repetition rates. Optimum dosages mayvary depending on the relative potency of individual oligonucleotides,and can generally be estimated based on EC5Os found to be effective inin vitro and in vivo animal models. In general, dosage is from 0.01 μgto 100 g per kg of body weight, and may be given once or more daily,weekly, monthly or yearly, or even once every 2 to 20 years. Persons ofordinary skill in the art can easily estimate repetition rates fordosing based on measured residence times and concentrations of the drugin bodily fluids or tissues. Following successful treatment, it may bedesirable to have the patient undergo maintenance therapy to prevent therecurrence of the disease state, wherein the oligonucleotide isadministered in maintenance doses, ranging from 0.01 μg to 100 g per kgof body weight, once or more daily, to once every 20 years.

In embodiments, a patient is treated with a dosage of drug that is atleast about 1, at least about 2, at least about 3, at least about 4, atleast about 5, at least about 6, at least about 7, at least about 8, atleast about 9, at least about 10, at least about 15, at least about 20,at least about 25, at least about 30, at least about 35, at least about40, at least about 45, at least about 50, at least about 60, at leastabout 70, at least about 80, at least about 90, or at least about 100mg/kg body weight. Certain injected dosages of antisenseoligonucleotides are described, e.g., in U.S. Pat. No. 7,563,884,“Antisense modulation of PTP 1B expression,” incorporated herein byreference in its entirety.

While various embodiments of the present invention have been describedabove, it should be understood that they have been presented by way ofexample only, and not limitation. Numerous changes to the disclosedembodiments can be made in accordance with the disclosure herein withoutdeparting from the spirit or scope of the invention. Thus, the breadthand scope of the present invention should not be limited by any of theabove described embodiments.

All documents mentioned herein are incorporated herein by reference. Allpublications and patent documents cited in this application areincorporated by reference for all purposes to the same extent as if eachindividual publication or patent document were so individually denoted.By their citation of various references in this document, Applicants donot admit any particular reference is “prior art” to their invention.Embodiments of inventive compositions and methods are illustrated in thefollowing examples.

EXAMPLES

The following non-limiting Examples serve to illustrate selectedembodiments of the invention. It will be appreciated that variations inproportions and alternatives in elements of the components shown will beapparent to those skilled in the art and are within the scope ofembodiments of the present invention.

Example 1 Design of Antisense Oligonucleotides Specific for a NucleicAcid Molecule Antisense to a Reprogramming Factor and/or a Sense Strandof a Reprogramming Factor Polynucleotide

As indicated above the term “oligonucleotide specific for” or“oligonucleotide targets” refers to an oligonucleotide having a sequence(i) capable of forming a stable complex with a portion of the targetedgene, or (ii) capable of forming a stable duplex with a portion of anmRNA transcript of the targeted gene.

Selection of appropriate oligonucleotides is facilitated by usingcomputer programs that automatically align nucleic acid sequences andindicate regions of identity or homology. Such programs are used tocompare nucleic acid sequences obtained, for example, by searchingdatabases such as GenBank or by sequencing PCR products. Comparison ofnucleic acid sequences from a range of species allows the selection ofnucleic acid sequences that display an appropriate degree of identitybetween species. In the case of genes that have not been sequenced,Southern blots are performed to allow a determination of the degree ofidentity between genes in target species and other species. Byperforming Southern blots at varying degrees of stringency, as is wellknown in the art, it is possible to obtain an approximate measure ofidentity. These procedures allow the selection of oligonucleotides thatexhibit a high degree of complementarity to target nucleic acidsequences in a subject to be controlled and a lower degree ofcomplementarity to corresponding nucleic acid sequences in otherspecies. One skilled in the art will realize that there is considerablelatitude in selecting appropriate regions of genes for use in thepresent invention.

An antisense compound is “specifically hybridizable” when binding of thecompound to the target nucleic acid interferes with the normal functionof the target nucleic acid to cause a modulation of function and/oractivity, and there is a sufficient degree of complementarity to avoidnon-specific binding of the antisense compound to non-target nucleicacid sequences under conditions in which specific binding is desired,i.e., under physiological conditions in the case of in vivo assays ortherapeutic treatment, and under conditions in which assays areperformed in the case of in vitro assays

The hybridization properties of the oligonucleotides described hereincan be determined by one or more in vitro assays as known in the art.For example, the properties of the oligonucleotides described herein canbe obtained by determination of binding strength between the targetnatural antisense and a potential drug molecules using melting curveassay.

The binding strength between the target natural antisense and apotential drug molecule (Molecule) can be estimated using any of theestablished methods of measuring the strength of intermolecularinteractions, for example, a melting curve assay.

Melting curve assay determines the temperature at which a rapidtransition from double-stranded to single-stranded conformation occursfor the natural antisense/Molecule complex. This temperature is widelyaccepted as a reliable measure of the interaction strength between thetwo molecules.

A melting curve assay can be performed using a cDNA copy of the actualnatural antisense RNA molecule or a synthetic DNA or RNA nucleotidecorresponding to the binding site of the Molecule. Multiple kitscontaining all necessary reagents to perform this assay are available(e.g. Applied Biosystems Inc. MeltDoctor kit). These kits include asuitable buffer solution containing one of the double strand DNA (dsDNA)binding dyes (such as ABI HRM dyes, SYBR Green, SYTO, etc.). Theproperties of the dsDNA dyes are such that they emit almost nofluorescence in free form, but are highly fluorescent when bound todsDNA.

To perform the assay the cDNA or a corresponding oligonucleotide aremixed with Molecule in concentrations defined by the particularmanufacturer's protocols. The mixture is heated to 95° C. to dissociateall pre-formed dsDNA complexes, then slowly cooled to room temperatureor other lower temperature defined by the kit manufacturer to allow theDNA molecules to anneal. The newly formed complexes are then slowlyheated to 95° C. with simultaneous continuous collection of data on theamount of fluorescence that is produced by the reaction. Thefluorescence intensity is inversely proportional to the amounts of dsDNApresent in the reaction. The data can be collected using a real time PCRinstrument compatible with the kit (e.g.ABI's StepOne Plus Real Time PCRSystem or LightTyper instrument, Roche Diagnostics, Lewes, UK).

Melting peaks are constructed by plotting the negative derivative offluorescence with respect to temperature (−d(Fluorescence)/dT) on they-axis) against temperature (x-axis) using appropriate software (forexample LightTyper (Roche) or SDS Dissociation Curve, ABI). The data isanalyzed to identify the temperature of the rapid transition from dsDNAcomplex to single strand molecules. This temperature is called Tm and isdirectly proportional to the strength of interaction between the twomolecules. Typically, Tm will exceed 40° C.

Example 2 Modulation of a Reprogramming Factor Polynucleotide Treatmentof HepG2 Cells with Antisense Oligonucleotides

HepG2 cells from ATCC (cat#HB-8065) were grown in growth media (MEM/EBSS(Hyclone cat #SH30024, or Mediatech cat #MT-10-010-CV) +10% FBS(Mediatech cat# MT35-011-CV)+ penicillin/streptomycin (Mediatechcat#MT30-002-CI)) at 37° C. and 5% CO2. One day before the experimentthe cells were replated at the density of 1.5×105/ml into 6 well platesand incubated at 37° C. and 5% CO2. On the day of the experiment themedia in the 6 well plates was changed to fresh growth media. Allantisense oligonucleotides were diluted to the concentration of 20 μM.Two μl of this solution was incubated with 400 μl of Opti-MEM media(Gibco cat#31985-070) and 4 μl of Lipofectamine 2000 (Invitrogencat#11668019) at room temperature for 20 min and applied to each well ofthe 6 well plates with HepG2 cells. A Similar mixture including 2 μl ofwater instead of the oligonucleotide solution was used for themock-transfected controls. After 3-18 h of incubation at 37° C. and 5%CO2 the media was changed to fresh growth media. 48 h after addition ofantisense oligonucleotides the media was removed and RNA was extractedfrom the cells using SV Total RNA Isolation System from Promega (cat#Z3105) or RNeasy Total RNA Isolation kit from Qiagen (cat#74181)following the manufacturers' instructions. 600 ng of RNA was added tothe reverse transcription reaction performed using Verso cDNA kit fromThermo Scientific (cat#AB1453B) or High Capacity cDNA ReverseTranscription Kit (cat#4368813) as described in the manufacturer'sprotocol. The cDNA from this reverse transcription reaction was used tomonitor gene expression by real time PCR using ABI Taqman GeneExpression Mix (cat#4369510) and primers/probes designed by ABI (AppliedBiosystems Taqman Gene Expression Assay: Hs00602736_s1, Hs00358836 m1,Hs03005111_g1 by Applied Biosystems Inc., Foster City Calif.). Thefollowing PCR cycle was used: 50° C. for 2 min, 95° C. for 10 min, 40cycles of (95° C. for 15 seconds, 60° C. for 1 min) using Mx4000 thermalcycler (Stratagene).

Fold change in gene expression after treatment with antisenseoligonucleotides was calculated based on the difference in18S-normalized dCt values between treated and mock-transfected samples.

Results

Real time PCR results show that the levels of SOX2 mRNA in HepG2 cellsare significantly increased 48 h after treatment with two of the siRNAsdesigned to SOX2 antisense ai885646 (FIG. 1A).

Real time PCR results show that the levels of KLF4 mRNA in HepG2 cellsare significantly increased 48 h after treatment with two of the oligosdesigned to KLF4 antisense. (FIG. 1B).

Real time PCR results show that the levels of POU5F1 mRNA aresignificantly increased in HepG2 cells 48 h after treatment with some ofthe antisense oligonucleotides to POU5F1 natural antisense AI926793(FIG. 1C).

Although the invention has been illustrated and described with respectto one or more implementations, equivalent alterations and modificationswill occur to others skilled in the art upon the reading andunderstanding of this specification and the annexed drawings. Inaddition, while a particular feature of the invention may have beendisclosed with respect to only one of several implementations, suchfeature may be combined with one or more other features of the otherimplementations as may be desired and advantageous for any given orparticular application.

The Abstract of the disclosure will allow the reader to quicklyascertain the nature of the technical disclosure. It is submitted withthe understanding that it will not be used to interpret or limit thescope or meaning of the following claims.

What is claimed is:
 1. A method of upregulating a function of or theexpression of a Reprogramming factor polynucleotide selected from SEQ IDNOS: 1,2 or 3 in mammalian cells or tissues in vivo or in vitrocomprising: contacting said cells or tissues with at least one singlestranded antisense oligonucleotide 14 to 28 nucleotides in lengthwherein said at least one oligonucleotide is specific for a naturalantisense polynucleotide of said Reprogramming thetor polynucleotide andhas at least 90% sequence identity to a reverse complement of saidnatural antisense polynucleotide comprising 10 to 30 consecutivenucleotides within nucleotides 1 to 993 of SEQ ID NO: 4, 1 to 493 of SEQID NO: 5, and 1 to 418 of SEQ ID NO: 6; thereby upregulating a functionof and/or the expression of the Reprogramming factor polynucleotide inmammalian cells or tissues in vivo or in vitro.
 2. A method ofupregulating a function of and/or the expression of a Reprogrammingfactor polynucleotide selected from SOX2, KLF4 or POUF51 in mammaliancells or tissues in vivo or in vitro comprising: contacting said cellsor tissues with at least one single stranded antisense oligonucleotide14 to 28 nucleotides in length wherein said at least one oligonucleotideis specific for a natural antisense polynucleotide of said ReprogrammingFactor polynucleotide and has at least 90% sequence identity to areverse complement of a natural antisense of a Reprogramming factorpolynucleotide; thereby upregulating a function of and/or the expressionof the Reprogramming factor polynucleotide in mammalian cells or tissuesin vivo or in vitro.
 3. A method of upregulating a function of and/orthe expression of a Reprogramming factor polynucleotide selected fromSOX1, KLF4 or POU5F1 in mammalian cells or tissues in vivo or in vitrocomprising: contacting said cells or tissues with at least one singlestranded antisense oligonucleotide of 12 to 28 nucleotides in lengththat specifically targets and hybridizes to a region of a naturalantisense polynuelcotide of the Reprogramming factor polynuceotideselected from SEQ ID NOS: 4, 5 or 6; thereby upregulating a function ofand/or the expression of the Reprogramming factor polynucleotide inmammalian cells or tissues in vivo or in vitro.
 4. The method of claim3, wherein a function of and/or the expression of the Reprogrammingfactor is increased in vivo or in vitro with respect to a control. 5.The method of claim 3, wherein the at least one antisenseoligonucleotide targets a natural antisense sequence of a Reprogrammingfactor polynucleotide having SEQ ID NO:
 4. 6. The method of claim 3,wherein the at least one antisense oligonucleotide targets a naturalantisense polynucleotide antisense to coding nucleic acid sequences of aReprogramming factor polynucleotide.
 7. The method of claim 3, whereinthe at least one antisense oligonucleotide targets a natural antisensepolynucleotide having overlapping sequences with a Reprogramming factorpolynucleotide.
 8. The method of claim 3, wherein the at least oneantisense oligonucleotide comprises one or more modifications selectedfrom: at least one modified sugar moiety, at least one modifiedinternucleoside linkage, at least one modified nucleotide, andcombinations thereof.
 9. The method of claim 8, wherein the one or moremodifications comprise at least one modified sugar moiety selected from:a 2′-O-methoxyethyl modified sugar moiety, a 2′-methoxy modified sugarmoiety, a 2′-O-alkyl modified sugar moiety, a bicyclic sugar moiety, andcombinations thereof.
 10. The method of claim 8, wherein the one or moremodifications comprise at least one modified intemucleoside linkageselected from: a phosphorotlnoatc, alkylphosphonate, phosphorodithioate,alkylphosphonothioate, phosphoramidate, carbamate, carbonate, phosphatetriester, aeetamidate, carboxymethyl ester, and combinations thereof.11. The method of claim 8, wherein the one or more modificationscomprise at least one modified nucleotide selected from: a peptidenucleic acid (PNA), a locked nucleic acid (LNA), an arabino-nueleic acid(FANA), an analogue, a derivative, and combinations thereof.
 12. Themethod of claim 1, wherein the at least one oligonucleotide comprises atleast one oligonueleotide sequences set forth as SEQ ID NOS: 7 to 17.13. A method of upregulating a function of and/or the expression of aReprogramming factor selected from SOX1, KLF41 or POU5F1 in mammaliancells or tissues in vivo or in vitro comprising: contacting said cellsor tissues with at least one short interfering, RNA (siRNA)oligonucleotide 19 to 30 nucleotides in length, said at least one siRNAoligonucleotide being specific for a natural antisense polynucleotide ofa Reprogramming factor polynucleotide, wherein one strand of said atleast one siRNA oligonucleotide has at least 80% sequencecomplementarity to at least about 19 nucleotides of said naturalantisense polvnucleotide and, upregulating a function of and/or theexpression of a Reprogramming factor in mammalian cells or tissues invivo or in vitro.
 14. The method of claim 13, wherein saidoligonucleotide has at least 90% sequence complementarity to saidnatural antisense polynucleotide.
 15. A method of upregulating afunction of and/or the expression of a Reprogramming factor selectedfrom SOX1, KLF4 or POU5F1 in mammalian cells or tissues in vivo or invitro comprising: contacting said cells or tissues with at least onesingle stranded antisense oligonucleotide of about 16 to 30 nucleotidesin length specific for as natural antisense strand of as Reprogrammingfactor polynucleotide wherein said at least one antisenseoligonucleotide has at least 80% sequence identity to at least onenucleic acid sequence set forth as SEQ ID NOS: 1 to 3 or an RNAtranscribed from the Reprogramming factor polynucleotide; and,upregulating the function and/or expression of the Reprogramming factorin mammalian cells or tissues in vivo or in vitro.
 16. A method ofpreventing or treating a disease associated with at least oneReprogramming factor polynucleotide and/or at least one encoded productthereof selected from SOX1, KLF4 or POU5F1, comprising: administering toa patient a therapeutically effective dose of at least one singlestranded antisense oligonucleotide of 10 to 30 nucleotides in lengththat specifically binds to a natural antisense sequence of said at leastone Reprogramming factor polynucleotide selected from SEQ ID NOS: 4, 5or 6 and upregulates expression of said at least one Reprogrammingfactor polynucleotide; thereby preventing or treating the diseaseassociated with the at least one Reprogramming factor polynucleotideand/or at least one encoded product thereof.
 17. The method of claim 16,wherein a disease associated with the at least one Reprogramming factorpolynucleotide is selected from: abnormal Reprogramming factorexpression and/or function, cancer, a renal disease, a cardiovasculardisease or disorder, inflammation, a neurological disease or disorder,scarring, ophthalmic diseases or disorders selected from microphthalmia,coloboma, myopia, anophthalmia/microphthalmia—esophageal atresiasyndrome, Septooptic dysplasia, an autoimmune disease or disorder,diabetes, atherosclerosis, an immunodeficiency disease, a disease causedby infectious agent including, viral, bacterial, fungal, protozoan, agenetic disease selected, from Duchenne muscular dystrophy, a metabolicdisease or disorder selected from diabetes, obesity, metabolic syndrome,lysosomal disease, trauma selected from spinal cord injury, burns;ischemia, a vascular disease, a hepatic disease or disorder, Psoriasis,a disease, a disease or disorder requiring transplantation of cells,tissues, and organs, disorder or condition requiring stem cell therapyand a congenital disease or disorder.
 18. The method of claim 1, whereinthe at least one oligonucleotide comprises at least one oligonucleotidesequences set forth as SEQ ID NOS: 7 to 17.